By design, you cannot directly deposit a payment from a client to your bank account. The payment first has to be deposited into an Undeposited Funds account and then transferred to the relevant bank account.
An invoice payment debits your 'Undeposited Funds' account and credits your A/R account. When the funds are deposited, the Undeposited Funds account is credited and your bank account is debited. You can see more of the accounting behind a transaction by viewing the journal entries or the Journal report in Core. Check out the Core Help for more details on the Payments screen.