i suck at DIY projects, so wish I could say I could help. When buyinig the product, you are really on your own unless you can get somebody with experience to help you or just do it themselves.
I'd try removing the stuff in chamber three so it just has the pump in there, and see if you can accomodate the skimmer in there. chamber 2 should suffice with rubble and the macro algae you have growing back there.