Stripe for online payments. Quickbooks is synced to a 3rd party scheduling software. Stripe deposits show as additional sales. Should I delete them OR create GL OR rule?

Hello user20115, 

If these deposits are duplicate transactions then we can delete (exclude) them. On the other hand, if they are already recorded in QuickBooks then we can match them. If not, we can add them to your bank's register. 

Please refer to this article for more information on how to manage downloaded banking transactions. 

I would also recommend reaching out to your accountant if you'll enter them through a General Ledger. They can help you identify what accounts you'll associate to these transactions. 

If you want to create bank rules for these transactions, you follow the steps provided in this article: How to set and use banking rules for downloaded transactions.

Reach out tome if you need more help.