How can I use baseline security with SUS?
You'll need to use some other method in addition to SUS. SUS does a good job of grabbing the correct patches for computers, but Baselining is something completely different. You need to get an accurate inventory of the computers that are installed in your organization. There are several apps on the market that will do it, and also several scripts out in the public domain. Additionally, if you roll your computers out using images, you could verify that the images are up to date prior to deploying new computers.
In a nutshell -- SUS by itself will not give you the "snapshot" you need to generate a proper baseline.