You should be able to accomplish this by using the SQL Compare (and possibly SQL Data Compare) command line.
You'll need to create two xml files and reference them from the command line.
If you go into your extended properties for the database you're working with, you'll notice "SQLSourceControl Scripts Location" and "SQLSourceControl Migration Scripts Location". You'll need to pull the value from SQLSourceControl Scripts Location and create an xml file with that value and also create a separate xml file for the value of SQLSourceControl Migration Scripts Location.
In your command line, you'll need to include these switches:
/migrationsfolderxml:filepath for migration scripts xml
/scriptsfolderxml:filepath for scripts xml
Here's the documentation page for using the command line for SQL Compare: http://documentation.red-gate.com/displ ... mmand+line
There are a few less complicated worked examples here: http://documentation.red-gate.com/displ ... mmand+line
Hope that helps,