If you can catch them it would be a good idea to take the fish out. There is a good chance they will die from the cycle and most people regret damsels later anyway. They can be very aggressive. Your tank can cycle with new live rock or a small piece of shrimp.
As for the refugium. You can put some live rock rubble in there and some macro algea to help reduce phospates and nitrates. They are also a great place to have your pods multiply. A heater on a controller would be a good idea as well.
I have the RK2 and love it. I highly recommend it. The guys that run the company are great. If there is something you want it to do that it doesn't they will try to figure out a way to add that to the next software upgrade.
There is a thread going in RC right now where it seems to be about 50/50. However, I thought mine was fine until I saw him try to tear off a piece of clam. So some of those may just be in denial.
Sorry about the Blenny. However, I am of the "feed heavy, Skim heavy, do large water changes" opinion. I feed about 3 times a day. I have never had a fish get over weight.
I'm not sure if this is what you are asking, but I know that at least with my RO unit I get 4 gallons of waste water for every 1 gallon of RO/DI water.
I just waited until the cycle was finished. Be careful not to add too much at once though or you will start a new one. How about some pics of your set-up?
Clint, I just found this very interesting article about clam care that talks about these snails and treatments. Check it out:
http://www.reefkeeping.com/issues/2006-09/jf/index.php