Hi Ann,
My recommendation is to omit the Paypal fee on the Sales Receipt and deposit the Sales Receipt directly to the Paypal account (assuming you have changed the preference to no longer default to Undeposited Funds.) This saves a step and saves you time. It also gives the donor full credit for the donation and posts the gross amount as a deposit into Paypal. Since the Paypal account is a bank account, as previously recommended, use the Write Check screen to record the payment of fees to Paypal. Reconcile regularly just as you would any bank account. There are reports available on Paypal that are similar to bank statements.
For existing Sales Receipt transactions in QB, if you went through Undeposited Funds, QB will make you delete the Deposit before you are allowed to edit the Sales Receipt to remove the negative line. If you did not go through Undeposited Funds and instead posted the Sales Receipt directly to the Paypal bank account, you will be allowed to edit the Sales Receipt.
I hope I've been clear. Let me know if not. Good luck!
