Motivated by recent experiments studying the dynamics of configurations bearing a small number of vortices in atomic Bose-Einstein condensates (BECs), we illustrate that such systems can be accurately described by ordinary differential equations (ODEs) incorporating the precession and interaction dynamics of vortices in harmonic traps. This dynamics is tackled in detail at the ODE level, both for the simpler case of equal charge vortices, and for the more complicated (yet also experimentally relevant) case of opposite charge vortices. In the former case, we identify the dynamics as being chiefly quasi-periodic (although potentially periodic), while in the latter, irregular dynamics may ensue when suitable external drive of the BEC cloud is also considered. Our analytical findings are corroborated by numerical computations of the reduced ODE system.