The_Engineer said:
Since this is a 2nd order vector differential equation, should it be equivalent to a system of two 1st order ODEs or four 1st order ODEs?
In theory, the answer is yes. In practice, when using numerical techniques, the answer is a resounding no.
Here's the theory. Create a phase vector that contains the position and velocity vectors. This new vector contains 2N elements, where N is the dimensionality of the space. For your 2D problem, this combined position+velocity vector is ##\vec u = [x,y,\dot x, \dot y]##. The derivative of this 4-vector is another 4-vector: ##\dot{\vec u} = [\dot x, \dot y, \ddot x, \ddot y]##. You already know the first two elements, and you also know the next two via ##F=ma## (presumably you know the net force).
You have a 4-vector and you a way to calculate its derivative, so just use your favorite numerical first order ODE technique to integrate. Easy!
Not so easy. The problem is that this approach ignores the geometry of the problem. If you can find a 2nd order ODE solver that is of the same degree as that 1st order ODE solver, the 2nd order technique is almost always going to be better because it pays at least some attention to the geometry.
A simple example: The simplest 1st order ODE technique is the explicit Euler method for 1st order ODEs. A much improved (but still lousy) technique that pays attention to the 2nd order nature of F=ma is the symplectic Euler method. Explicit Euler doesn't conserve any of the conserved quantities (energy, angular momentum, and linear momentum). Symplectic Euler comes much closer to doing so.
Don't use either of the Euler methods. Symplectic Euler is lousy; explicit Euler is extremely lousy. You still need to understand the Euler methods because all but the most advanced techniques are variations on the Euler methods. A slight step up in complexity is the leapfrog / verlet family of integrators. Done right, these require only one computation of acceleration per time step, but the accuracy is vastly improved. There is no 1st order ODE equivalent to any of the leapfrog / verlet integrators.
You can do even better than this, but now things get complex. There is a problem with higher degree geometric integrators: They get hairy.