Let me help you with reconciling the account, Gaslite.

The transaction will only be marked when you select it. You can leave the Checks and Payments section unmarked by not selecting any transactions, then select the deposits only. 

Although, if you've selected some transactions already, you'll have to unmark them manually. 

I'll share the reference on how to reconcile an account in QuickBooks Desktop for more details. 

Visit the Community if you have other questions. We'd be happy to hear from you again.