Thanks for the help. I initially thought I would do the checkout route where you type how much you want to pay...but I'm all about convenience and if the buyer doesn't know how much they owe, that's a problem. People lose paper invoices all the time and email invoices can get deleted by accident.
What I'd really like is a payment management system. On my end, I can enter amounts owes for each customer. Then, on the website, the form asks for their customer number and a password. This will lead them to a payment portal where they can see their balance, what they have been charged for (invoice breakdown) and then pay. Almost like online electricity bill pay.