Level 4

How to Record Bank Deposits in QuickBooks Online

I am working with a nonprofit which has been depositing checks and assigning the customer directly to each deposit line. I have always been told you should issue an invoice or process as a Sales Receipt. This method does show up on P&L by customer/job but there is nothing in the customer record so none of the other customer reports work and nothing shows up in the customer center.  Still, they do see it on the customer or job P&L. Am I wrong to recommend (strongly) that they issue invoices or Sales receipts?