If you want to use points, you have to book through MS. You don't even have to book on board as the on board credit will not carry over to a points booking. Reportedly, you now have 7 days after the end of the cruise to call MS to book a new cruise a get the rebooking discount using points. Also, any cash portion will be due in full at the time the booking is made.
we cruised on points once. We did look at booking another cruise with points. Only because you could save about 14/person while booking while being on board. But as far as I know, you have to book with points pay the rest in cash, if that is what you want to do.
We recently booked a cruise while onboard the Fantasy. You have to pay the 10% deposit. You then have seven days from the end of the cruise to convert to points or points/cash. You MAY get a reduction in points by booking on board--we got a 3% reduction. If you pay for part in cash, you pay in full at the time. You do lose the OBC.