I'm a new quickbooks user, but this seems like something that shouldn't be troubling. I have created invoices, and began to recieve payments for them, but how I am entering them appears to make them 'double entered'. Once I recieve a payment from someone, I go to customer payments and enter that they have paid, so the invoice gets stamped 'paid'. The check is still in my hand, but quickbooks shows it as already there (in accounts recievable). Then I go to the bank, actually deposit the money, and then enter that deposit directly into the registry. Now that money is showing up a second time (in the operating account).
So if I invoice someone for $100, once the paid stamp appears on their invoice, it shows that there is $100 in that account. Then I deposit the money to the bank, and record the deposit in the registry for $100. Now that specific account shows the $100 deposit... totaling $200... $100 from accounts recievable, and $100 from the deposit at the bank.
I'm sure this is a very simple problem and there's just one step that I'm missing, but I dont' know what it is.