There's nothing special you need to do - the "in excess of basis" amount only affects the basis schedule, not the depletion schedule. The full amount of depletion automatically carries to the depletion schedule.

So if you have a K-1 that shows 
percentage depletion: $100
depletion in excess of basis: $70

Your depletion schedule shows the full $100 of depletion. Your basis schedule reduces basis by only the net $30.