You need to Control this: "how can I receive deposits and not have this happen everytime"
If you are a cash basis reporting entity, that is Income. Use a prepayment service or other charge item for that. If you are an Accrual Basis entity, that is a Liability, so link your charge item to Liability or Income, to meet your accounting needs.
When someone gives a Prepayment deposit, use Sales Receipt with that prepayment item.
When you are done, you charge them on an Invoice. Use that prepayment item on a Credit Memo for the date of the invoice, with the amount they prepaid, to apply it to reduce the total owed, the Balance Due, on the invoice. This reflects that you applied their prepayment to the Total sale.
