As Joel said, "don't throw anything out!" And don't cut any more until you reach the "ah ha" stage. It's all about the reference faces and getting themm right with each other. As long as your joinery is layed out from the reference, the wood on the non-reference side doesn't need to line up. Your reference is almost always the outside surface and one other surface or the outside and a centerline. In either case you are referencing in two dimensions, creating a reference "edge" or intersection of the two reference planes. This intersection is your arris and it allows you to line up with the arrises of other members.
It is like riding a bike for the first time- suddenly everything clicks and it works! If you can get the chance to work with someone who is familiar with square-rule, it will come quickly.
Get to a Guild workshop of rendezvous- you'll find the experience immeasurably valuable. Good luck.
