I am confused about what are the points of the topological space $|X|$ underlying a scheme $X$. When $X = \textrm{Spec}(A)$ is affine, the points of the topological space are just the prime ideals of $A$.
The cause of the confusion is the idea of geometric points, which are morphisms from Spec of an algebraically closed field to $X$. I don't think these are points of the underlying topological space $|X|$ in general. So my question is: can the points of $|X|$ be described in terms of the functor of points approach? (I mean the points of $|X|$ correspond to morphisms $\textrm{Spec}(K) \to X$ for what fields $K$?)
A scheme is "locally affine". That means if I take any point $p\in X$, there is an affine open neighborhood $U$ containing $p$, say $(U,\mathscr O_X|_U)\cong(Spec(A),\mathscr O_{Spec(A)})$. Therefore $p$ corresponds to some prime ideal $\mathfrak p\subset A$. This is often the way you work with the points in a "hands on" way while doing problems. So for instance, the stalk at $p$ is $\mathscr O_{X,p}\cong A_{\mathfrak p}$.
Unfortunately, I don't think I have a good response to the second part of your question. Hopefully somebody else will.