Use a condition to limit the databases a policy checks
You can certainly limit the set of databases that are checked, using a condition, and have that condition be separate from the actual condition the policy is using to check. Pull down the "Every" drop-down in the UI:



Create a new condition:



Then you should be able to use that condition:



Note that this is using the SQL Server 2012 version of Management Studio (which is now completely free, as of SP1). If the UI does not behave this way in the 2008 R2 version of the tools, upgrade your tools.