You can lay it out with holes for say 7805 form-factor regulators even if you plan to power it from a bench supply at this point. You don't have to populate them, it won't cost any more to have the boards made and you will be ready to experiment with regulators when you want to.

One thing you have to worry about with programmable logic is supply sequencing: the overall timing of voltage rails coming up to nominal when power is turned on. This can be an issue when the start-up speeds vary, which is something you can see easily on a scope.

I usually power my prototypes from my bench power supply. As you say, it saves picking a VReg at this stage. Yes, you should have a nice meaty capacitor where the power enters the board.