I have the same setup. I do live rock rubble in chamber one, then I use a sponge on the waterfall in chamber two to catch the big stuff. Easier than floss and you just rinse it and put it back in to clean it. Also the top of the sponge being "dry" makes it a great catch all. Chamber two also has a tunze skimmer. Then in chamber three I took out the foam block and put a bag of carbon and phosphate absorption media there. This way the cleanest water is forced through your expensive media. Note: If you do the skimmer option you also will need a auto top off for the system to really work. Even if you don't get a skimmer...get a auto top off, I avoided it for years but ever since I have had one my life is soooooo easy. With this system I often leave my 29 unattended for 2 weeks at a time.
Nick