Sounds like you and I are in the same boat, NaCL-Man. I've done pretty much the exact same thing as you and found the same thing with my skimmer. Man, the stuff that it pulls outta the tank stinks big time! I have been cleaning mine out every day just to get rid of the stench.
To answer your question, movadoman, yes...keep your skimmer running all the time. I would second the motion to get yourself some good reading material. It helped me out a lot, as did this site. Good luck!!!