Hello there, @DynamoBicycle.

I'm here to share some pointers to resolve this deposit fee in QuickBooks Merchant.

Yes, fees associated with the invoice should be recorded as a separate transaction. You'll need to tap the link for each invoice to enter the difference manually. This way, you'll be able to avoid discrepancies when you start reconciling your books.

Furthermore, you can refer to the steps provided by @Rose-A above on how to track bank fees or deposit charges. 

I'm adding this article for your additional guide to reconciling an account in QuickBooks Online.

You can use various reports and forecasts to get a complete image of your company's current and future finances. You can get some ideas from this article: Track your cash flow in QuickBooks Online. 

Feel at ease if you need assistance with how to run an invoice report. I'll be here around to guide you always. God bless you.