drill holes big enough to just get the wire through, then just nail in cord runners to neaten everything up when you finish.
How many lights are you installing?
I would think 2 ceramic edison fittings, and a fluro on the other side would be fine, only need 1 hole big enough to get all 3 wires through.
Edit: Oh, i know what you mean about there being a gap between the light and the walls, you might want to bolt the lighting to a piece of timber that matches the rest of the tank, then drill your holes through it and rout them to the board. Then screw that piece of timber with the light fitting attached to the roof of your enclosure. Might be a bit tricky to picture in your head, i can get a photo of mine if you like.