AppleTV, iTunes and Multiple Disks
What I would do is:


Have only 1 library
Make sure that iTunes is configured to keep all your media organized (and point your single iTunes Library to your preferred disk)
When adding files to your iTunes library hold down Option/Alt to let iTunes know that it shouldn't copy the file to where your library is


This way all your data will be organized by iTunes except for the large files that should belong on your largest external disk in the first place.

Cheers...