The game will usually automatically put the conference logos on the jersey and the field when you import (as long as you don't already have something there).
You have to choose the prestige sliders based on the options. I wish you could manually adjust them all, but the options you have to choose from are pretty solid imo.
Biggest thing with Team builder dynasties is the crashing issue that happens. I cannot finish the first game in my team builder dynasty. I'll get somewhere in the second half and it crashes randomly...