I have a non-b which requires me to leave the country every 3 months. What happens if I leave the country before the 3 months are up? When I re-enter do they use the remaining days from the previous term or do I start a new 3 month term?

Every entrance date on a multi-entry-non-immigrant visa starts a new 90 days. If you enter on the day before your visa expires you still get 90 days (and thus the visa can basically be used for 15 months). If you leave after the last day on your VISA but before your permission to stay expires then you will need a new visa to get 90 days.