Good morning, @ccassetti,


Thanks for the question!  Let's dive into this.  When you said you changed over the Intuit deposits, did you change the fees, as well?  If you didn't, that may be why you're running into this issue.  This article may help with selecting accounts to record the deposits and fees:


Choose where to record payments and processing fees for QuickBooks Payments


Once you've done that, let me know if there's any difference.  I'm here to help!