Consider $F = -\nabla U$ a conservative force field in $\Bbb R^3$. Assume we describe the motion of a unit mass particle under this force field by a curve $q(t) = (q^1(t), q^2(t), q^3(t))$. We have Newton's law $$-\frac{\partial U}{\partial q^i}(q(t)) = \ddot{q}^i(t), \quad i=1,2,3,$$which is a second order differential equation in $\Bbb R^3$, and we want to convert that into a first order differential equation in $\Bbb R^6$ by calling $p^i \doteq \dot{q}^i$, so that we have $$\begin{cases} \dot{q}^i(t) = p^i(t) \\[1em] \dot{p}^i(t) = -\dfrac{\partial U}{\partial q^i}(q(t)), \end{cases}$$great.
Question: How can I write indices according to Einstein's summation convention (for psychological reasons, I'll still write summations signs)? The index $i$ in $p^i$ is covariant or contravariant?
If $i$ goes "in the ceiling" as $p^i$, then $\dot{p}^i = -\partial U/\partial q^i$ is bad.
If $i$ goes "in the cellar" as $p_i$, then $p_i = \dot{q}^i$ is bad.
Is there an identification being made? If $M$ is a manifold and $(U, (x^i))$ is a chart, then $(TU, (x^i, \xi_i))$ is a chart in $TM$, and since we see $\Bbb R^6$ as $T\Bbb R^3$, this would indicate to use $p_i$. I'm confused.
In symplectic mechanics, the components of $p$ are local coordinates for the cotangent bundle, so a physicist would "naturally" write them with subscripts. Consequently, you need to invoke the metric $g_{ij}$ to relate $\dot{q}$ and $p$. For instance, Hamilton's equations for the Hamiltonian $$H(q,p)=\tfrac{1}{2m}p_{i}g^{ij}p_j + U(q)$$ are $$\begin{align}\dot{p}_i&=\tfrac{1}{m}p_lg^{lk}\Gamma^j_{ki}p_j-U_{,i}\\ \dot{q}^i&=\tfrac{1}{m}g^{ij}p_j \end{align}$$ where $\Gamma$ is the Christoffel symbol for $g$.
More stuffily, we say that $(\dot{q},\dot{p})$ is the Hamiltonian vector field associated with the function $H$.