The previous person in our company set up our factored receivables wrong. Do I go in and do a general journal entry for the accounts or do I correct each deposit?

Welcome to the Community, @thelacebuckaroo.

I would love to help you, but I just need more specific information so I can address your concerns properly. May I know how you set up the factored receivables? 

Any additional information would help me check for solutions to address your concerns better. Please don't hesitate to provide any further details or a screenshot as a visual guide to explain your scenario more clearly.