I used water based stain on my canopy. I DO NOT IN ANY WAY like the finish it gave the wood. I should have just paid to have the color matched by a painter. I took a piece of wood into HD and had them color match it. I ended up with water based stain, and I HATE the finish up close. It looks like the stain is sitting on top of the wood, not penetrated into it.
Back to your origional question.
Is your tank on the stand right now? Does the tank have any inhabatants? IF not, go ahead and do what you want. wear a respirator (osha made me say that....) and stain away.
If you have animals in your tank, you might want to cover the tank for the first few hours, and also shut off your protien skimmer. Sucking the fumes directlyinto the water column is a bad idea.
I would move the canopy away from the tank, even if you have creatures in your tank. No chance of drips gettinginto the tank then.
It is better if you point the fan IN to bring in more fresh air, it will dilute/disperse the bad fumes better than just one fan pointing out trying to suck the bad stuff out. One fan in and one fan out at opposite ends of the room is the best way to get rid of fumes with just fans
Just my 2c.
Brett