The problem with the pads (if you know already, sorry, but I wanted to explain it just in case) is that they trap gunk and poop and crap and food. The water still flows through the pads though. So the gunk dissolves and breaks down, but the water passing through it just washes it back into the tank. The garbage is never physically removed from the tank by the filter. Also, the bacteria that convert nitrate (bad) to nitrogen gas (so it can escape the tank) are anaerobic. The pads do not provide an anaerobic environment for that bacteria to live, so you are lacking that final component needed to complete the nitrogen cycle. Those two factors are how nitrogen tends to build up. If you use lots of live rock (1 to 2 lbs per gallon) its effects are lessened, because the live rock usually provides a bit of anaerobic space for the bacteria to live. A protein skimmer physically removes the crap into a separate collection cup for you to throw away, so that's why protein skimmers are so much better than filters.
