You can drill it while it is filled with H2O. It's been done before. That being said, as you don't have much in there I would transfer everything over to your sump (as Jason said, a 10g or 20g tank work just fine) and then you could drill the tank while it's dry.
What are you planning on housing in your sump? Skimmer, refugium, heater, return pump??? This will give you an idea of how large it should be and how you should lay it out.
Garrett.