Not sure what you don't understand, the wiki, or downloads.txt?
Copy downloads.txt from the ulx addons directory mentioned above to your server gmod/data/ulx/ folder.
Then only edit the new file just copied.
If you have special files, whether they are in addon package or not, the server sees them as gmod root/<whatever>/<whatever_files>, not gmod root/addons/<whatever>/<whatever_files>
If you wanted to share an entire folder, you'd copy that folder to your server host as always (perhaps including an addons/<blah>/special_folder, but, to your fastDL (and our downloads.txt), it would never include the "addons", it would simply be <fasdl>/<blah>/special_folder and in downloads.txt, <blah>/special_folder
If you you wanted to share a particular file within <blah> (Blah being sounds, materials, models, other common gmod file folders), you'd still upload the file to your server as always (even if in addon format), then upload the file to your FastDL host /blah/special_folder/whatfile.blah folder, and the in downloads.txt, you'd place blah/special_folder/whatfile.blah