Yes. You just have to be booked at the hotel to receive the benefits. If your confirmation number doesn't link to your Disney account, call the hotel directly and ask them for a different one that will work. If you have the reservation linked to your account, you will be able to use the 60-day Fastpass benefit.
Just word of caution, I booked B Resort using the Mousesavers discount. It took me over two weeks before my reservation number would link to my Disney account. I tried the confirmation number from B over and over. I called Disney, and they told me to wait a few more days and then call B if it still wasn't working. I called B and they gave me a completely different confirmation number to try. That still didn't work. I was about to call B again today, but tried linking one last time. The original number I had finally worked. It might take some persistence, but don't get discouraged if it doesn't link right away.