Yes, thats exactly what you do. You actually don't need two versions. All you need is the install. Music and videos are optional. All you need to copy are the various files with the .avi extension. I'll provide a list for you.
AVIs
CEP, CES, CPP, CPS, e4, I, IE, IP, MEBL, MEBW, MEF, MEUL, MEUW, MPBL, MPBW, MPF, MPUL. *
*Note, there are files with the .dll extension with the same name. You do not need to worry about those! They already come in the download.
Music
OP2.clm*
music1.wav**
*In game music
**Menu music.
I also think I've figured out some of the initials, assuming they ever where supposed to mean anything.
I = Introduction
E = Eden
P = Plymouth
F = Final
Thats all I think is "for sure". B, U, W, L, not so sure about. I think W = Win and L = Lose or Loss, or something like that. Not sure what the B and U would mean, though.