This is the kind of thing you should really work out with a client before you take the job. No matter how you structure the payment it's important to be really clear what things will cost. At this point, one way you could do it is to keep a record of the hours you worked each day and what you did on the project, and post it online for your client to see. That would avoid any surprises. Then total up the hours and send an invoice at the end of the month. (You can find templates for invoices in programs like Microsoft Word which you can customize with your own information and logo). Or you could work out a overall project cost and divide that up into monthly installment payments.
I also send my clients things like playblasts, pre-renders, and model renders to keep them up to date. That way they can tell you early if you're going in the wrong direction. Also, if you can get a client really excited about a project he may even expand it and increase the budget! I've had that happen many times.