I have a red sea prizm deluxe also. It will take a few days to run in and requires continuous fine tuning. I have not found anyway of eliminating the micro bubbles, but I had some success by placing a piece of filter foam in the media basket. This seems to reduce the bubbles a bit.
It will again take a good day for it to skim again if you have cleaned the collection cup. Any water changes and after feeding will stop the skimmer from skimming for a few hours.
I found the best skimming position is to have the water level at the rubber ring level of the collar or just above. And the surface skimmer is absolutely useless. I uses a separate surface skimmer instead of the supplied one.
Mine is skimming quite well, but it takes patience and fine tuning. My LFS
has two installed in their tanks, and they do skim really nasty stuff. My SG