If someone is setup on autopay, will it pay all of the invoices that are due?

Yes.  If you go to Tools from the main menu and then click on the Settings tab, and then click on "Fee Types" it will list all of the fee types you have setup in the system. There is a column on that page called "Subject to Autopay" which allows you to check a box next to each fee type that you would like to be subject to an owners autopay setting. For example, IF someone has a "special assessment" fee type enabled to be subject to autopay and an owner has autopay enabled for his/her unit, THEN the special assessment will automatically be attempted to be paid on the due date of the special assessment fee type invoice.