Checking if some software is installed or not, getting the compliant or not-compliant status, creating Dynamic Computer Collections based on this status and applying Software package can be ideal solution for your environment.
But let's start.
In this example I will check if FCS ForeFront client is installed or not.
First lets create Configuration Item:
Click Next and Close.
Next Step is to create Configuration Baseline where the previous FCS Installed created Configuration Item will be included.
Write the name of Configuration baseline. In this case it is FCS Installed Baseline.
Choose Application and General and right from the list choose FCS Installed.
Click Next and after that Close.
Next step is to assign this Configuration Baseline to Computer Collection but to avoid applying the Configuration Baseline on All System computer collection you can create a Dynamic Computer Collection. I've published an article where I created a dynamic collection based on string included in computer name:
Here is the Part 2 from this article: http://tompopov.blogspot.com/2011/05/desired-configuration-management_24.html