I don't think there really is an easy way to do this. Certainly it's not a feature of Font Folio.
As a work-around, I'm wondering if you might pop in the CD, then use Windows' Search to search the CD for *.pfm and *.pfb, this would eventually list all the .pfm and .pfb files in the search window, where you could then select them all and copy them into a new folder on your desktop (or elsewhere). Once you'd done that, you could then go into ATM and browse to that desktop folder to install everything in one fell swoop.
Option 2 would be to simply install individual font families from the CD as you want/need them. Font Folio has a lot of fonts, you certainly wouldn't want them all active in any case--if only for the sheer annoyance of picking the font you want from a never-ending list.