To be technically accurate, you are not balancing them separately, you're balancing them both at the same time along two different axes. Let me set up a system so I can type this with a chance of being understood. Visualize the prop horizontal. Now think of it in three pieces - the left blade, the hub, and the right blade. Now:
Case 1: Let's say the left blade is "heavy." In that case, we'd sand a little behind the blade until it balanced out. Since everything else was OK, it will not spin in the balancer no matter what orientation it starts from - a perfectly balanced prop.
Case 2: Left blade heavy, bottom of hub heavy. We would need to sand the heavy blade until it stayed horizontal in the balancer. Then we would add some glue (or whatever your fav method is) to the top side of the hub so that when you orient the prop vertically in the balancer, it stays put.
Case 3: Left blade heavy, left side of hub heavy. In this case, you would sand extra on the blade to get it to stay level. You think that it's just a blade badly out of balance - but you have no way of knowing that the hub was contributing. It doesn't matter. It will be balanced and not vibrate due to imbalance.
Case 4: The bottom edge of the left blade is heavy, hub balanced. Again, you can't know what part of the blade is heavy. You sand the blade to fix it horizontally, then you add glue to the hub to fix it vertically, not knowing that it was the blade that was making it not stay vertical in the balancer. Again, it doesn't matter as far as the shaft is concerned.
Well, I've probably confused things tremendously, but all I'm trying to say is that "prop" then "hub" balancing is just making sure that the whole system is balanced about the shaft while rotating.