Live rock is great to use as a filter, you just have to keep it clean, as liverock in the back chambers will settle detritus back there, and detritus turns into nitrates and phosphates over time (simplification). You can keep it back there for now to seed the tank (which works out well too as if there is any photosynthetic algae on those rocks, it'll die off and won't spread to your main rocks), and then once the tank has been up a month or more, you can remove the rocks. Just make sure to siphon out the rear chambers periodically with water changes. I just do my entire water change from the back chambers and siphon off of the bottom the whole time.
Just whatever you do, don't throw those pieces of live rock away! I need them now to glue new corals too, and you will too once your tank grows out more.