I realize this is not documented terribly well. The pond fraction for each category, i.e. apond00n is exactly as it sounds. It is the fraction of ponds in that ice category. So, to get the pond fraction on the ice covered portion of the cell it is:
aice001*apond001 + aice002*apond002 + ... + aice005*apond005
To get a pond fraction relative to the whole gridcell, you would then divide by aice. In 1850 control integrations we see very little pond coverage in the Arctic. This is because most of the snow is sticking around through the summer. In the latter part of the 20th century runs we get better fractions of up to 0.2 in the Beaufort Sea. It is usually still low in the central Arctic. There is some internal tuning that can be done here. The runoff fraction (rfrac) is one of the main things that improves pond coverage. Currently it is set to a minimum of 15% for aice=~1, and a max of 85% for aice=~0. The other tuning in ice_meltpond.F90 is how much of the ponds affects the albedo when there is snow in the gridcell. When the snow depth exceeds 3cm, the ponds do not show through at all.
Dave