The reloading lever only makes the crossbow ready to fire the next round from its case
The repeating crossbow's full description:
The repeating crossbow (whether heavy or light) holds 5 crossbow bolts. As long as it holds bolts, you can reload it by pulling the reloading lever (a free action). Loading a new case of 5 bolts is a full-round action that provokes attacks of opportunity.
You can fire a repeating crossbow with one hand or fire a repeating crossbow in each hand in the same manner as you would a normal crossbow of the same size. However, you must fire the weapon with two hands in order to use the reloading lever, and you must use two hands to load a new case of bolts.
When it says that you may reload the crossbow by pulling the reloading lever, it means that you can prepare the crossbow to fire again using the next bolt in the currently loaded case, as the crossbow cannot automatically load itself and draw its own string. Think of it like a firearm with a manual action, like a pump-action shotgun. It might have several rounds in its magazine, but you have to manually cycle the action to chamber the next round and cock the firing hammer - which is effectively what the reloading lever does for the repeating crossbow, dropping the next bolt into the crossbow's groove and drawing back the bowstring.
There's no action given for adding single bolts by hand to the crossbow, only that it's a full action to replace the case/magazine of bolts. Depending on the design of the crossbow it might or might not make sense to be able to load extra bolts by hand - if you could, loading an extra bolt that way should probably be a move action, as if you were loading a light crossbow by hand:
You draw a light crossbow back by pulling a lever. Loading a light crossbow is a move action that provokes attacks of opportunity.
A heavy crossbow nominally requires a full-round action to load, but even a heavy repeating crossbow can apparently be drawn using the reloading lever as a free action rather than requiring a winch, so I wouldn't rule it to be more difficult to load by hand than a light crossbow is.