I am still looking for a solution to this issue. I have dozens of cash transactions imported from Square and placed into Payments to Deposit (Undeposited funds). Of those, I deposited $252 in cash to our business checking account and left the rest (many other transactions) for petty cash. The $252 does not align neatly with any selection of the cash transactions that I can find, so at least one of those small transactions (we sell coffee) was partially deposited. I've tried adding the smallest additional transaction to the match and then clicking Resolve and adding a transaction back into Payments to Deposit, but this then shows up as an expense.

So is there no easy way to get Quickbooks to account for a perfectly legal and common use case: depositing only a portion of a cash transaction?