Whenever I set up new EoF projects I always "Use Source Audio Folder".
If you do this then you can make a new folder (call it "EoF for Bonus" or something), copy and paste the notes.eof and the guitar.ogg into it, load it up and edit/save as necessary. This copies over your existing beat map and notes, which can then be easily copied and pasted about to create the arrangement you desire.
Because you have essentially 2 separate EoF projects running with the same charts, and saving into their own folders by default, then I find this the easiest way to increase the track count.
Just make sure that when you build the custom using the toolkit that you point the toolkit to the correct XML arrangements from the different folders.
I know there will be multiple ways of making the same end result, I just find this the easiest and safest way.