I had a bare bottom tank for a long time. You have to get a powerhead to move the waste over. Put it on the opposite side of your filter intake and it should blow the waste into the intake.
IMO, bare bottom isn't worth it. You can get pretty much the same results if you add a thin layer of sand into the tank. Either way, the fish waste will move towards your filters, but the sand will make your tank look 10x better.