I can't comment on rewards stay upgrade but...
.... we recently stayed at the property (March 7-10) in a cottage room using the Sip and Savor package. I have stayed at the property many times and in a number of different rooms/cottages and they are basically the same. I found that booking the cottage room actually became a source of stress for me because I had certain expectations but the reality is that you may get a cottage that faces the parking lot, and then it is a little disappointing. Or you want an upstairs room but you don't get one. It goes on and on.
All I can say is that you won't be disappointed with anything that faces the interior gardens, whether you are in the main building or in a cottage. I would ask for an upgrade via the virtual concierge although I did contact requesting an upper cottage room and we did not receive it. I don't remember if/when you said you were going. I was stunned at how crowded the place was so I hope you are going during a time that is less crowded so your chances of an upgrade are greater.
BTW, the only benefit to the S&S package was the free breakfast; our daily tab would have been $45-50. Enjoy - Sonoma is gorgeous.