When you start SQL Compare, you will be prompted to register servers.  The first thing you need to do is uncheck integrated security.   I could not get this to work and received error messages every time I tried.   After setting it to standard security, enter your server name and the database to use as the source.  When you click OK, SQL Compare will connect to the server and extract scripts from the database you selected.  I didn't like this.  Script extraction should not be performed until I tell it to actually run a compare.  This limits the functionality to immediate, one shot compares.  You will then input the same information for the server and database to compare to.  When you click OK, it will immediately extract scripts from that server and compare to the first one.   Again, this is rather limiting and should be an area to improve upon for future releases.

When the compare completes, you will see something similar to the figure below.   An equal sign indicates there is no difference.  A right pointing, blue arrow indicates the object exists on the source server, but not the destination.  A left pointing, red arrow indicates an object that exists on the destination and not the source.   A dual arrow indicates there is a difference.  From here you can highlight an object and view the source to compare differences.

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