Ok so, I've got a custom quest, and I've got a custom quest script, and they seem to have pretty arbitrary FormID values... Does it actually matter what their FormIDs are, or does that influence combatibility with other things? For example, could they be 00000000 and 00000001 without causing any trouble?

Queue

Its best to let the GECK decide.

But, you can never have a form ID of 00000001 because the first two digits are always replaced by the load order number of your mod in the game. And the last mod loaded in always wins if there is a compatibilliy issue. Note that the save game is ALWAYS last and will override any mod if the data is stored in the save game. (whats called a dirty save game)