Maybe just put a little trap door in the top to do water changes, float bags, etc with.
Mine canopy has everything crammed in there so I really couldnt do it once it was said and done.
You need to get an oil based paint. Exterior use. The kind that has mineral spirits in it.
You wont find a non-toxic paint. The key here is just to make sure it drys really well before going over the tank (obviously if you put it on while its a little wet you will have fumes inside the canopy that would take a while to get out, not to mention maybe paint dripping)
Once it is dry its as safe as you can get.
I thinned about 50% paint thinnner 50% paint in a cup and painted about 3 coats of "primer" (The wood soaks up alot of paint) then did about 3 coats of the regular paint. Its water proofed now!
Be sure to get high-gloss. It acts as a reflector and will bounce more light back into the paint (You wont see it so color wont matter)
For the outside I did about 3 coats of the clear protector after staining it.
Hope this helps you a bit!
I recessed my top peice of plywood and made a little "groove" all around inside the top edge, and dropped the peice of wood in the top. Made it look pretty nice.