I think that the best input for a skimmer is unfiltered water coming straight from the tank and thats it. So, no other filtration, no chemicals, or anything else should touch the water before it enters the skimmer (some people use a filter sock before, that's ok). I know that just dropping some food in the water, or putting my hands in the tank can cause the bubble column to collapse, so its pretty sensitive.
I have 2 10gallon tanks, one sump and one refugium. But I used to have just 1 10gallon. What I did was use some pieces of glass as baffles to form 3 chambers and keep everything seperate. First chamber was for overflow from tank and skimmer, which overflowed into the second (middle) chamber where the refigum was, which then went through a bubble trap into the third chamber where only the return pump was.
I would recommend at least putting the chemical media after the skimmer and away from any flow that the skimmer will in take. Also, the chaeto should be kept seperate as well if you can.
How is everything set up now?