Both tools should have come with documentation. If they didn't, find a good mirror of the Geek Gadgets ftp site (like back2root.orgs) or try browsing
http://www.geekgadgets.org through
http://www.archive.org.
fd2pragma is more flexible than fd2inline. You only need hunk2aout if you want to link Amiga hunk files with gcc a.out files, but it sounds like that's what you want to do.
Trev