I've replicated your concern, Pammyq88.
When you send invoices on the Income Tracker window, it will immediately let you send the transactions. Though, whatever template is used, that's the same template your customer will receive.
In QuickBooks, you'll have to create invoices so you can send them to your customers. You have the option to memorize an invoice for your regular customers. This way, a transaction is automatically created when it's due. You can check this article for more information: Create and modify memorized transactions.
If you need more help, you can always get back to this thread.
