We receive payments from the State of Michigan for invoices and quickbooks automatic download will use the same invoice name on multiple payments, how do I correct that?

In QBO you receive invoice payments against invoices outside the bank feed and deposit them to the undeposited funds account. Then you create deposits from undeposited funds to match the deposits that come into the bank feed. While you can find matching invoices for a deposit that comes into the QBO bank feed, it is not advisable to do the transactional accounting this way, as it makes it harder to reconcile, as the bank statement deposits amounts will not consistently match. Be careful to not start adding deposits directly from the bank feed without following the correct accounts receivable process.