If the payments are going into Undeposited Funds, it sounds like the payments are coming to you and your showing payments against invoices. This is actually the way QBs normally work.
So backing up a bit to pre QBs or any other kind of computer bookkeeping program... When payments came in the Invoice was marked paid and that money did not go directly into the bank. In fact a trip to the bank might only be once a week or some other period of time. So to balance the books when an Invoice was paid, all the money went into an Undeposited Fund Account. Then when there was a Deposit made, there would be an entry made showing the funds moving from the Undeposited Acct to the Bank Account.
There are ways to change this, but the process is still in QBs. It basically goes like this:
Check received from Client. Invoiced marked as Paid and the counter entry QBs makes is to show the money in the Undeposited Funds Acct. When you make a deposit, you go to Banking > Make Deposit and you'll be shown all the payments that have been placed in the Undeposited Funds. From there you pick what you are depositing and which Bank Account it is going into. (And check the date if you making this entry before/after you really made the deposit.)
And don't just check everything to get it out of Undeposited Funds, You need to match it with what you really deposited. You'll see that the Bank Account shows those deposits and that will be what you're trying to match up with the Bank Sync. You can sit down and make these deposits any time you want, but it's best to make them before you Sync with your bank. But even if you don't you can make the entries without an issue as long as you do not Accept the items in your Bank Sync first. That's when you need to start deleting and adding back in.
