You don't create More JE.

@IamjuViel

Please Learn from the input here. JE should be Avoided for anything where Names are involved.

@batvalil

They are not used for AR, AP, you cannot list Items, they are not going to show as sales or allow for sales taxes, not for QB payroll. Worse, you just bypassed Cash vs Accrual Basis reporting. Your income tax reporting in those prior years might be horribly wrong. Let's review.

"I have close to $100k in credit balances."

This is where Cash vs Accrual is the issue; Negative AR does not show as Income for the financial reporting, and if some of that is Sales tax liability, that isn't getting any details about the funds from a corresponding Invoice details, at all.

"In looking at what the prior "accountant" did I can determine the following -  A journal would be booked (instead of creating an invoice) debiting A/R and crediting the income account.  The customer name was noted in the memo line."

QB requires a Name in the Customer Field, if they posted to "AR"; otherwise, you would use your own Generic Other Current Asset.

"When the payment was received a customer account was created  and the check was received against the customer account; however, there were no invoices to post these checks against because the invoice was created with a journal entry."

You would be able to Apply them to each other if there was a Name in the Income JE for the AR line. If there is not a name, they didn't use "real AR" and that means, you can create an Other Charge Type item linked to that Other Current Asset account and put that on an Invoice for the customer now, dated historically for that JE. Apply the Available Credit to the Payment. Now you are Clearing that Other Current Asset Balance and applying the Negative AR from the checks.