Try Carbon in the first chamber.
A skimmer isn't going to solve your problem. In my humble opinion in a 12G with low stock you don't have enough live stuff generating waste to need a skimmer. Water changes will help you.
You may also have micro bubbles. This will decrease over time but the water should not fall from chamber 2 to chamber 3 where the return pump is. If it does, you will get microbubbles via the return.
I use one of these in the first chamber. I emptied the filter media and just use filter floss that I change out weekly. It doesn't do too much, but the floss does get gunked up so its obviously working.
http://www.marinedepot.com/ps_Aquar..._oscar_enterprises_mini_micro_dive_clean.html