The chaeto in chamber 2 is great but it produces a lot of little particles or maybe detritus just collects in the back chambers and gets shot out into the main display. Bubbles are not the issue.
Since I put floss in the little compartment in chamber 3 (where the sponge was) and put a big bag of carbon in chamber 2 --I've seen fewer particles.

How do you keep your water clear?

I use good old poly-fill from Hobby Lobby. Are you using a media basket? If not get one from Steviet at http://mediabaskets.com/ The trick is to not over fill the poly-fill section of your media basket. If you over fill the water runs over top of the poly-fill. You want the water to fall through the poly-fill. If that makes any sense.