I don't think I know of anything that doesn't. While I know as a user we can cause blunders that the developers never even imagine possible I can't think of a single feature that would break just because you go to a custom layout.
I think as long as you move along slowly and test things out as you go you shouldn't have any problems. You also have a forum full of people that can answer most questions if you do happens to forget a tag and something stops working the way you expected it to.
--
Six Demon BagJack Burton: Hey, what more can a guy ask for?
Egg Shen: Oh, a six-demon bag!
Jack Burton: Terrific, a six-demon bag. Sensational. What's in it, Egg?
Egg Shen: Wind, fire, all that kind of thing!