And this part here is an error: "I listed each donor and the date and amount of the donation, including the PP fee with a negative number (-0.74)"
The Donor gave you that Gross amount. The Banking or PP fee is Yours, not theirs. It doesn't reduce Donation. It reduces Banking. Your Gross Donation is a Net to Bank.
"now i have those donations showing in my Make Deposits window and I wouldn't be making a deposit to our bank account with those."
Go to Edit menu > Preferences, Payments on the left, then Company Preferences tab on the right. Remove the checkmark for "Use UF as my default."
Now the top of the Sales Receipt offers "Deposit To:" and you select Pay Pal Bank. You get a statement from PP and you track this Gross Deposit into PP bank. You use Banking menu > Write Check to enter that the PP Bank, top left, incurred a Banking Fee. Now you reconcile this PP Bank to the PP statement. And yes, you Transfer funds to checking when you want to Move Funds from PP to Checking. This is not when you got the income. This is just banking.
And you will also Make Deposit for those historic Sales Receipts, now, to the PP bank. But fix them and Remove your Banking fee.
