You are able to accept a payment for an order on the Checkout Tab in an order and you can also resolve a payment on the Accounts Receivable Report.
You are able to add in as many payment types as you would like (Customize > BPro Settings/Location Builder > Edit > Payment Types). Our defaults are Cash, Check, Debit, Credit - Visa, Master Card, Amex, Discover, and Account if you have it enabled for your customer.