I did as was suggested above: 

Donor gave $51.50

I add to the deposit a (-)1.50 to ensure the deposit matches the actual bank deposit, and record the amount received for the fees.  

when I go to reconcile I have the correct deposit, but the fee is showing as an expense to clear? How to clear these in reconciliation?

Then my fee account has both a deposit AND an expense - doubling the amount of the fees - when in fact it should zero out?

what am I missing?