The main reason for using 2 pads is so you can do a pad change safely.
Since most of the bacteria resides in the pad, removing all of it at once might trigger a new cycle. <Yes, the bacteria is also on your ornaments, etc .... but lets say you have a bare bottom tank ....> Having 2 pads allows you to change out one pad, and have the new pad seeded from the old so there is no risk of a cycle.
So go ahead & run both pads. Clean as usual. When one pad is falling apart, change it for a new one. Leave the old one in for a least 3-4 weeks to make sure the new pad is sufficiently colonized. <If you stagger the pads right, you will prob. be changing out one pad every 6 month or more.>
As for carbon, it is effective only when fresh. I tend to treat carbon as just another surface for the biofilter. <Carbon might even be better than some of the bioballs, etc as a bio-media substrate.> If I need to use carbon to pull out med, etc. I put in fresh as needed.