My doubt is very general but I'm going to give an example so I can explain why I'm struggling with this.
I have a 2-form $\alpha$ written in Cartesian coordinates
$$ \alpha=\alpha_{ij}\,dx^i\wedge dx^j $$
If I want to integrate this on a 2-sphere $S^2\in\mathbb R^3$, I'm going to change $\alpha$ to spherical coordinates $(x,y,z)\to(r,\theta,\phi)$ and have something like this
$$ \int_{S^2}\alpha= \int \alpha'_{\theta\phi} \,d\theta \wedge d\phi $$
But I know that $d\theta \wedge d\phi=-d\phi \wedge d\theta $, so I also have
$$ \int_{S^2}\alpha= -\int \alpha'_{\theta\phi} \,d\phi \wedge d\theta $$
Which is the correct way to integrate $\alpha$ over $S^2$?
$$ \int_{S^2}\alpha= \int \alpha'_{\theta\phi} \,d\theta \,d\phi \quad\text{or}\quad \int_{S^2}\alpha= -\int \alpha'_{\theta\phi} \,d\theta \,d\phi $$
I can't discern difference between the two integrals, I need a procedure to choose the correct way to integrate. And the thing is worse when I'm trying to integrate things less intuitive and with other manifolds.
I don't find any source either with clear examples and where I can understand
Suppose $M$ is an oriented $m$-dimensional manifold and $\alpha$ is a smooth compactly-supported $m$-form on $M$. Then, we can consider its integral $\int_M\alpha$. Note that this integral depends on the choice of orientation for $M$. For simple examples like balls, ellipsoids, (one half of) hyperboloids, paraboloids or their boundary surfaces, we can usually use a single chart $(U,\psi)$ to cover the entire manifold, up to a "negligible set". If the chart is orientation-preserving, then we can write \begin{align} \int_M\alpha&=\int_U\alpha=\int_{\psi^{-1}[\psi(U)]}\alpha=\int_{\psi(U)}(\psi^{-1})^*\alpha\tag{$*$} \end{align} where on the RHS, $(\psi^{-1})^*\alpha$ is an $m$-form on an open subset $\psi(U)$ of $\Bbb{R}^m$, and thus can be written as $(\psi^{-1})^*\alpha=f\,dx^1\wedge \cdots \wedge dx^m$, where $(x^1,\dots, x^m)$ is the usual cartesian coordinate chart on $\Bbb{R}^m$ (and thus $dx^1\wedge \cdots\wedge dx^m$ is indeed the volume form), and for a unique function $f:\psi(U)\to\Bbb{R}$. So, we have \begin{align} \int_M\alpha&=\int_{\psi(U)}f\,dx^1\wedge \cdots \wedge dx^k:=\int_{\psi(U)}f, \end{align} where the last symbol is a Riemann/Lebesgue integral of a function $f:\psi(U)\to\Bbb{R}$, i.e a standard integral. So far, all I've done is chase definitions.
As a remark, if $\psi$ is an orientation-reversing chart, then we must modify $(*)$ to \begin{align} \int_M\alpha&=\int_U\alpha=\int_{\psi^{-1}[\psi(U)]}\alpha=-\int_{\psi(U)}(\psi^{-1})^*\alpha. \end{align}
Now, let us recall how we can induce orientations. Suppose $(M,g)$ is an $m$-dimensional oriented Riemannian manifold with Riemannian volume form $\mu$. Let $S$ is an $(m-1)$ dimensional embedded submanifold (i.e a smooth hypersurface) which admits a smooth unit normal vector field $n$ (i.e $n:S\to TM$ is a smooth map such that for each $p\in S$, we have $g_p(n_p,n_p)=1$ and for each $\xi\in T_pS$, $g_p(n_p, \xi)=0$). Then, we have the induced volume form $\mu_S:= \iota_S^*(n \lrcorner \mu)$, i.e the pullback to $S$ of the interior product of $n$ with $\mu$. This means, for each $p\in S$ and $\xi_1,\dots, \xi_{m-1}\in T_pS$, we have \begin{align} (\mu_S)_p(\xi_1,\dots, \xi_{m-1})&:=\mu_p(n_p,\xi_1,\dots, \xi_{m-1}). \end{align} In particular, what this means is $\{\xi_1,\dots, \xi_{m-1}\}$ is a positively-oriented ordered basis of $T_pS$ (i.e the LHS above is $>0$) if and only if $\{n_p,\xi_1,\dots, \xi_{m-1}\}$ is a positively-oriented ordered basis of $T_pM$ (i.e the RHS above is $>0$). (Also, $\mu_S$ is indeed the Riemannian volume form of $S$, relative to the pullback metric $\iota_S^*g$, because if we chose the $\xi$'s to be positively oriented and orthonormal, then the RHS is equal to $1$ by definition of $\mu$ being the Riemannian volume form of $M$).
For more details about orientation, you should consult any differential geometry book, for example Spivak or Lee (Chapter 15 of Intro to Smooth Manifolds)
Now, we come to the case of the sphere $S^2$ in $\Bbb{R}^3$. Note that $\Bbb{R}^3$ has the standard Riemannian metric \begin{align} g=dx\otimes dx+dy\otimes dy+dz\otimes dz \end{align} and volume form \begin{align} \mu&=dx\wedge dy\wedge dz \end{align} Now, introduce spherical coordinates $(r,\theta,\phi)$ on a certain open subset of $\Bbb{R}^3$. Then, a standard calculation shows (equality obviously only on an appropriate open set of $\Bbb{R}^3$) \begin{align} \mu&=r^2\sin\theta\,dr\wedge d\theta\wedge d\phi. \end{align} The sphere obviously admits a unit normal vector field, and by convention, we choose $n=\frac{\partial}{\partial r}$ (restricted to $S^2$) to be the "outward pointing" unit normal. By my remarks above, this induces an orientation on $S^2$ with the volume form (I suppress the pullback to a certain open subset of $S^2$ in the notation) \begin{align} \mu_{S^2}&=\frac{\partial}{\partial r} \lrcorner \,r^2\sin\theta\,dr\wedge d\theta\wedge d\phi\\ &=\sin\theta\,d\theta\wedge d\phi \end{align} (the $r^2$ becomes $1$ since when we pullback to $S^2$, the radius is $1$). The range of $(\theta(\cdot),\phi(\cdot))$ is the open set $A:=(0,\pi)\times(0,2\pi)\subset\Bbb{R}^2$, which means $\sin\theta>0$, and thus the differential form $d\theta\wedge d\phi$ defines the same orientation as $\mu_{S^2}=\sin\theta\,d\theta\wedge d\phi$. Therefore, the spherical coordinate mapping which identifies an open subset of $S^2$ with $A$ preserves orientation.
In short, once you pull everything back to $A$, you deal with $d\theta\wedge d\phi$ (I'm abusing notation slightly here, since throughout I've used $\theta,\phi$ to mean functions on an open subset of $S^2$, so logically speaking I should refer to the corresponding coordinate functions on $A$ as $\tilde{\theta}$ and $\tilde{\phi}$), and as I mentioned in my formula $(*)$ in the beginning, due to the orientation-preserving nature, we don't introduce any rogue minus signs.
Edit In Response to Comment.
I didn't want to have to do this initially because it would require us to introduce extra notation. One should always be careful of where each object lives. Recall that in general, when we say $(U,\psi)$ is a chart for an $m$-dimensional manifold $M$, it means $U\subset M$ is open and $\psi:U\to \psi[U]\subset \Bbb{R}^m$ is a mapping from the manifold to the cartesian space. Since $\psi$ maps into $\Bbb{R}^m$, we can consider its component functions $\psi(\cdot)=(x^1_{\psi}(\cdot),\dots, x^m_{\psi}(\cdot))$, so $x^i_{\psi}(\cdot)$ is the $i^{th}$ coordinate function of $\psi$ (it's what one might typically write as $\psi^i(\cdot)$, but let us stick to $x^i_{\psi}(\cdot)$).
Next, if $A\subset \Bbb{R}^m$ is an open set, when we speak of "cartesian coordinates on $A$" what we mean is the identity chart $\text{id}_A:A\to A\subset\Bbb{R}^m$. In keeping with the above notation, $\text{id}_A(\cdot)= (x^1_{\text{id}_A}(\cdot),\dots, x^m_{\text{id}_A}(\cdot))$.
Now, when we speak of spherical coordinates on $S^2$, we're talking about a specific chart $(U,\psi)$. It is rather cumbersome to give the definition of $\psi$ (because inverting the trig functions is a little annoying). So, it is convenient to first define $A=(0,\pi)\times (0,2\pi)$ and consider the mapping $A\subset\Bbb{R}^2\to \Bbb{R}^3$, \begin{align} (\theta,\phi)\mapsto (\sin\theta\cos\phi,\sin\theta\sin\phi,\cos\theta) \end{align} The image of this mapping is an open set $U\subset S^2$, and the inverse of this mapping is called $\psi$. This is the definition of the chart $(U,\psi)$. What I've claimed above is that \begin{align} \mu_{S^2}&=\sin(x_{\psi}^1(\cdot))\,dx_{\psi}^1\wedge dx_{\psi}^2 \end{align} Notice that $\sin(x_{\psi}^1(\cdot))$ is a function $U\to\Bbb{R}$, and $dx_{\psi}^1$ is the exterior derivative of a function on $U$, and thus is a $1$-form on $U$ and so on. Thus, the RHS is properly a $1$-form on $U$.
To check that $\psi:U\to A$ is indeed an orientation preserving chart it means I have to take the volume form on $\mu_A$ and then show that $\psi^*(\mu_A)=(\text{strictly positive function})\mu_{S^2}$.
Now, $\mu_A=dx_{\text{id}_A}^1\wedge dx_{\text{id}_A}^2$ by definition. Let us now calculate the pullback of $\mu_A$ under $\psi$. For this, we need to recall that pullback commutes with wedge products and exterior derivatives: \begin{align} \psi^*(\mu_A)&=\psi^*(dx_{\text{id}_A}^1\wedge dx_{\text{id}_A}^2)\\ &=d(\psi^*x^1_{\text{id}_A})\wedge d(\psi^*x^2_{\text{id}_A})\\ &=d(x^1_{\text{id}_A}\circ \psi)\wedge d(x^2_{\text{id}_A}\circ \psi)\\ &=d(x^1_{\psi})\wedge d(x^2_{\psi})\\ &=\frac{1}{\sin(x^1_{\psi}(\cdot))}\,\mu_{S^2} \end{align} Since the sin is strictly positive here, we have indeed shown that $\psi^*(\mu_A)$ is a positive multiple of $\mu_{S^2}$, and thus $(U,\psi)$ is an orientation-preserving chart.
Prior to this edit, I called $x^1_{\psi},x_{\psi}^2$ as $\theta,\phi$ respectively, and $x^1_{\text{id}_A},x^2_{\text{id}_A}$ as $\tilde{\theta},\tilde{\phi}$. So, $\theta=\tilde{\theta}\circ \psi$ and likewise for $\phi$ (this is what I mean by non-tilde are functions on $U$ and tilde are the associated functions on $A$). So, \begin{align} \psi^*(\mu_A)&=\psi^*(d\tilde{\theta}\wedge d\tilde{\phi})\\ &=d(\tilde{\theta}\circ \psi)\wedge d(\tilde{\phi}\circ\psi)\\ &=d\theta\wedge d\phi\\ &=\frac{1}{\sin\theta}\mu_{S^2} \end{align} and this differs by a positive multiple from $\mu_{S^2}$, hence $\psi$ is orientation preserving.
Note that because the pullback operation is so natural and plays nicely with wedge products and exterior derivatives, we usually don't like to introduce excessive notation to distinguish between functions on $U$ vs functions on $A$ obtained by composing with the chart map $\psi$.