We numerically investigate an experimentally viable method, that we will refer to as the “chopsticks method”, for generating and manipulating on-demand several vortices in a highly oblate atomic Bose-Einstein condensate (BEC) in order to initialize complex vortex distributions for studies of vortex dynamics. The method utilizes moving laser beams (the “chopsticks”) to generate, capture and transport vortices inside and outside the BEC. We examine in detail this methodology and show a wide parameter range of applicability for the prototypical two-vortex case, and show case examples of producing and manipulating several vortices for which there is no net circulation, equal numbers of positive and negative circulation vortices, and for which there is one net quantum of circulation. We find that the presence of dissipation can help stabilize the pinning of the vortices on their respective laser beam pinning sites. Finally, we illustrate how to utilize laser beams as repositories that hold large numbers of vortices and how to deposit individual vortices in a sequential fashion in the repositories in order to construct superfluid flows about the repository beams with several quanta of circulation.