David,
I've been around VATSIM for a while now (but only seriously for about 18 months). I've got it figured out now, but I very much remember feeling exactly as you do. It wasn't the training part that confused me (that was easy once I was affiliated and talking to the guys at Miami). The hard part, as you so well described, was figuring out what to click and what comes next. As others have pointed out, the distributed nature of VATSIM organizations makes this difficult to figure out.
As a small example, one point of confusion for me was trying to discern the difference between VAT