my feeling is that there are many, many ways to accomplish the bio-fltration feat. Many hobbyist use bioballs/wet/dry, fluidized bed, LS/LR, the list is endless.
The keys are if you do use mechanical filtration (pads, bags, etc) ensure you clean it frequently, as Tony mentioned you want to clean off or remove the food and waste before it decays. Also if you use CC substrate you should really consider vaccumming it. If you use a DSB, you might want to include a sand bed cleaner.
As for cleaning pads, yes rinse them heavily to remove any decays waste and you can reuse them, Alternative, throw them out. depends on how much $$ you wanna spend.
In a well fed Fo tank expect nitrates and accept them, just ensure you are consistant and diligent in your cleaning and you'll keep them under control.
frank