If you use Virc's IDX extractor, you'll see the basic set-up of the files (it also includes a ReadMe).

Extract the skeletons and animations of vanilla/the mod you're modifying.
Add your new skeletons alongside the existing ones and the new animations in their proper subfolder (animators usually create their own folders for their work).
Then add the names of all your new skeletons at the bottom of list.txt and the names of all your new animations at the bottom of anim_list.txt.
Then put just pack_animations.bat, pack_skeletons.bat, xidx.shell and xidx.exe in the folder where the skeletons are and double click the two .bat files and you'll have your new .pak and .idx files.