IMO, without forcing the player to choose how many to reload, weapons reloaded one shot at a time could automatically 'complete' the weapon, using an amount of time proportional to the number of shots. If all shots don't fit, leave the extra ones in the original "clip item".
Ex. If a shotgun has 6 "spaces" and you shot twice already, when you drag 6 shells from a pocket to reload, it takes 1/3 of the time of a full reload, and leaves 4 shells in that pocket.
This behavior would avoid awkward situations where you have a near-empty shotgun, and the game forces you to unload before you can replace with a full group of shells.