No personal experience with Jetsetter, but suite upgrade certs can usually be applied towards reservations made through "regular" travel agents / third party suites, however some broker-like sites such as Priceline are excluded afaik, so you may want to ask the hotel.

If the Fairmont Savers Rate is sold directly be Fairmont, you should be able to apply a 3rd night free cert, however as getting a refund may be a bit of a hassle IŽd make that reservation over the phone. The Fairmont res agents tend to be very helpful and knowledgable IME.