An invoice can be paid directly from a trust account.  Under Invoices tab, in the listing on invoices for a case or a client, click on the green dollar sign (Pay Invoice).  In the pop-up box, check "Pay From Trust Account" checkbox and then select a trust account (if client funds are available in multiple trust accounts, all such accounts will be displayed). Click on "Record Payment".

After recording this payment, go to "Client" -> "Trust Transactions" to verify if the entry has been recorded against the selected trust account.  Don't forget to actually withdraw the money from the corresponding real bank account.