Hi Angela W,
Recording the PayPal fees for a nonprofit donation is a good exercise for keeping your books clean. I'd be happy to steer you in the right direction so you can focus on doing the things you enjoy.
To ensure accuracy in your books, I recommend contacting an accounting professional to get more info on recording the transactions. Doing this will help prevent any future discrepancies in your books. If you're not in contact with one, I encourage you to search for one on our website using this link here. In the meantime, check out this helpful article with more info on: How to record donations or charitable contributions.
I'll also leave this question here so other accounting professional members can chime in. Let me know if you have other questions. I'm here to help.