Can you not select payment within the I novice anymore. I hate the new invoice format

Are you asking if you can input the type of payment when accepting payments for invoices? Yes you can. On the app on a mobile device, complete your invoice and save it. This will kick you out of the invoice and back to the customer activity screen. Now reenter the invoice, click on more at the lower left corner, click on receive payment, click on record payment, now you are on what I will call the main payment screen. You can click on select payment method and this is where you get to select your type of payment. On the main screen you can also modify the payment amount if they are doing a partial payment. Finally, click on additional information and make sure that the account you are depositing to is correct. I use undeposited funds, so I always have to modify that. Click save and you will will be back to the invoice, with the payment applied. You can now email the invoice to the customer with zero or whatever balance is remaining. 

Is is a little easier on a computer. Get to your invoice list by clicking on all sales or invoices, then click on the invoice you are working on. In the right action column, click on receive payment, choose your payment method and destination account, modify the amount if you need to, and click save.