Payments are applied to the invoice to close the invoice as paid. These payments will be separated by the tender type that is accepted in your Clover account.
By default, all of the payments are associated to your Undeposited Funds account. You can open your Undeposited Funds account by going to the Chart of Accounts and double-clicking the Undeposited Funds account.
Payments will be associated to your Undeposited Funds account by default. You can change the Clearing Account in your Commerce Sync settings to map Credit Card, Cash, Checks and Other Payment Types to a different account.