It seems your question/concern has been answered but I just want to throw in my confirming 2-cents. :)

Although I got an electric three months before I finished Guitar Fundamentals, I played an acoustic all the way through levels 1 and 2 (the theory being the acoustic made me 'work' more). Once I started the next level of the Core Learning System I decided to try two tracks at once. In my morning practice session I do the "Country Style" set of tutorials and in my afternoon practice session I do the "Blues Style" set. In the morning I play the acoustic, in the afternoon I play the electric. Stuff like finger exercises, scales/CAGED-patterns, chord progressions and song accompaniment I split between the two guitars/practice sessions.

And it's a blast! :D