If I chose this ticket option, and use up my 4 days in the theme parks, once those 4 days are used, can I still use the tickets to get into the waterpark and Disney Quest?
Yes. Your ticket will expire 10 or 14 days(can't remember) after first day of use. You have each of the 4 park days and then the amount of options on it.
Yes. If your tickets are non-expiring, you can use those water park days any time. If not, you have to use them before they expire, but you can still use them until then.