Be prepared, you are about to get a thousand different ways to do this. You'll have to try many of the suggestions and in the end you end up using what works best for you.
Since I got here first, I get to start
First off I carefully choose not just what wood to use for each peice, but what section, grain pattern and such I want to show up for each piece.
I then (recently tried it and it works ohhh so good) put a layer of packing tape on the wood I'm going to use. I take my pattern and cut out each piece, but not exactly on the pattern lines. I leave just a little extra room that gets cut off and thrown away after cutting on the saw.
If I were going to do a quilt pattern, I might try to use the table saw to get symetrical and repeatable pieces. I think it would have a lot more character if each piece were cut on the scroll saw and then hand fitted, that way no matter where you look on the "quilt," it is a little different.
Tom