As far as the silicone goes, I left some wood bare so the silicone will stick nicely to the wood. Once the initial silicone cures, I will but a beam around the outside edge of the glass and when that is sured I eill seal everything by going from the tank, over the silicone and onto the glass with silicone. That should seal it up nice.
Yes, the sump will serve as both mechanical and biological. My only concern with the sump right now is that the holes in the drip plate will not be big enough for all of the water to pass through.