It's good to see you back, MichaelDougherty.

Yes, you can account the Stripe fee as a single expense. Just follow the steps provided by my colleague MaryLurleenM to create the deposit. 

Once done, you'll now be able to match the transaction created to the one downloaded from your bank on your bank feeds. See this guide when matching the transaction: Categorize and match online bank transactions in QuickBooks Online.

For future reference, you may find this link helpful: Setup bank rules to categorize online banking transactions in QuickBooks Online.

If you need further assistance when using QuickBooks, visit again in the Community space. I'll be more than happy to answer it for you. Take care.