Sorry guys, but you are both wrong!
First, do the *full* install, make everything maximum.
Next, copy all of the files from the 'resource' folders on the CD's, including both 'video folders', into the "[JK Path]\Resource" folder. Videos should all go in a single 'Video' subdirectory.
Finally, copy the "JK_.CD" file from the CD into the resource folder, and it should never ask for the CD again.
I've been doing this for comupters with no CD drive for years ... unfortunately MotS doesn't offer a no-CD, so I use Daemon Tools to mount the image.