Kyle,
On Arthur we have a manual pump who's hose goes to the deepest part of the bilge just aft of the keel void. I pump this out by hand when needed which up to now has only been after the ice melt from the fridge has drained out. It is a Titan whale gusher and can really move a lot of water in a hurry. Just to see what it could do I filled the bilge up with water and had it pumped dry in under two minutes.
http://images.westmarine.com/full/03525_f.jpg
We also have an electric bilge pump (Rule 2000 I think) mounted into the floor of the bilge using 3/16" SS screws. It sits below the sole access panel closest to the companionway. Does a Commander have two access hatches? The glass is thick enough there that 3/16" does not penetrate through and beside all you would go into would be the keel void which is dry as a bone right. Remember to mount the switch higher than the pump which is easy since the bilge floor slopes up fast right there.
I like this system because the electric pump stays high and dry 99% of the time but is there if needed. It is also easy to get to for inspection and cleaning. I have not measured exactly how much water has to be present to turn the bilge pump on but I ran a hose into the bilge after initial set up and I took a minute or two to "fill" the aft bilge to the turn on level. Some say you need two pumps, some more. I think that the important thing is to have at least one manual and one electric and of course one bucket.
Sounds like your windows need rebedding.We did it last year and it was a messy but straight forward job. Took all day to do the first two but an hour to do the last two! We bought a big 'ol piece of 1/2" Lexan from the local glass house and I cut the panes using the old ones as templates. I cut them out over-sized and did final shaping using my table top sander. Follow Lackey's advice and use longer screws and nuts during the initial set-up. Makes life a lot easier. I recommend using butyl I got mine at ACE. If you have time fill in the void between the inner and outer skins using the techniques described by Ebb. Makes for a tigher, cleaner final product. I remember the hardest part of the job was cleaning all the junk (Silicon 5200 buytl) off the old frames. Finally ended up using a wire wheel on my drill. Took it off pretty fast
Andrew