The symbols in the watch list are stored in the symbolconfig.xml file in the AppData directory (or whatever you specified with the /SettingsFolder command line option). So you can copy or edit that file.
An optimization plugin can control what symbols are used for the simulation, so that is one way to programmatically control what symbols are used for a system.
You can also programmatically modify the symbolconfig.xml file programmatically, but you have to do it outside of RightEdge since RightEdge only reads it when it starts up. I've attached some code that helps with this. WatchListObjects.cs contains the classes that are stored in symbolconfig.xml via XML serialization. WatchListUtil.cs use these classes to provide functions such as adding a list of symbols to a folder or deleting a folder.
RightEdgeLauncher is a program which allows you to type or paste in a list of symbol names and the launcher will create a folder with those symbols and then launch RightEdge with command/line options to update the data and or run a specified system with the symbols in that folder.
For a previous discussion of these topics, see here