Hi there, lbauer.
I appreciate you for providing detailed information with your concern.
Currently, there's no option to use a batch feature to enter deposits with several hundred line items in QuickBooks Online. Manually recording them is the way you can perform. Meanwhile, you can also use an app like the Transaction Pro importer tool that you've mentioned to help you do the things that you want to work on.
Then, once you manually entered transactions in QuickBooks Online, you can match them from downloaded entries to avoid duplicate data. Please click this article to see the process: Categorize and match online bank transactions in QuickBooks Online.
Please refer to this article to see how you can reconcile your accounts so they always match your bank and credit card statements to avoid discrepancies: Reconcile an account in QuickBooks Online.
Please let me know if there's anything I can help you with managing your bank transactions or other QuickBooks-related concerns. Take care and stay safe always.
