need help for client

I have a (corp) auto repair & body shop business w/2 locations and 12 employees. I do my own payroll and my version of QB consists of: bank rec, credit card rec, and loan balances. Our sales for both sides of business (body and mechanic) are manually entered into QB 1x monthly. Because each service has its own specialized software, we don't invoice through QB.

Every time at fiscal year, my accountant makes GJ entries that don't make sense.I don't understand receivables and still have credits to be assigned to customers invoices.My fiscal year runs Oct - Sept.(I use 1 customer "All Customers"and make a lump sum invoice for the whole month, splitting out sales and tax. Because this is a husband/wife owned corp, we commingle many accounts, yet try to keep to minimum,.