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You received checks to pay for invoices, do not worry about banking downloads
Use receive payments, check each invoice for that customer and receive the amounts. Make sure the account to be deposited to is undeposited funds.
then use make deposits when you get back from the bank. check off the two payments, select the bank account you deposited to, and insure the amount in QB matches the actual deposit, save.
THEN, when you download banking it just match the bank deposit to the QB deposit, if you use download banking.