I had the same question in my mind, and then realized it doesn't make much difference. When you're done fully raising the sail, the beads will actually go over the top and start down the other side. The first bead is for a reefed sail and the second one is for normal hoisting. Both are designed to hook on the front side of the sail and anchor it in place.
Going up or down they don't do much of anything. I've found that taking the sail down they can sometimes hook the top of the slot on the back side of the mast as they go into the track. Annoying but some up and down action will eventually get them settled.
It's probably better when they're in the track raising and lowering the sail, but it doesn't seem to make much difference.
Lubricating the sail where it goes into the track helps with hoisting. Last few feet are going to be difficult no matter what you do, as you've got a lot of friction from all the sail in the slot. It does help to experiment a bit with just the line and no sail. Those last few feet are a bit tricky and getting the knack of hanging the bead on the hook is hard on the eyes to see what's happening. Once you get the knack down, it's easy, but the first few times are a bit baffling.
Take a look at http://www.hobiecat.com/support/article ... ard-locks/
Also there is a video starring Matt Miller. See http://www.youtube.com/watch?v=1VeBZOCJCoY
Best of luck,