, I wouldnt worry about sealing the back completely. You are going to be putting plenty of silicone on the back to it just to seal it to the stick already.
As for leaving space.. other than the compartments or cut-outs you will create for your equipment, I wouldnt bother leaving any extra space. It isnt needed, and it could easily become an issue with fry getting trapped in there. The water that does get through wont be in any ammount that you need to wory about circulating, UNLESS you leave space for it to collect. Just put on a heavy amount of silicone on the back of your creation, and stick it to the glass.