Earlier today I was trying to book a weekend getaway and use up my annual free night certificate. I found a suitable SPG property but the website kept freezing up when I tried to make the reservation, so I gave up and called the elite reservations line. According to the customer service agent, the certificates are not good towards any of the SPG properties. When I expressed that I thought they were now merged and considered one entity, she told me, "not really - we're totally separate". It was the same response when I asked about using points.
It's not a big deal since I chose a Courtyard instead, but I thought I would save everyone else the hassle of trying to use points or certificates to book an SPG property. SPG properties will be listed in your results when you search for a stay using points, but apparently it's not do-able at this point.