@tlosm you need to have fs-uae *alongside* qemu-uae (i.e. projects/fs-uae, project/qemu-uae). See here:
http://eab.abime.net/showpost.php?p=976709&postcount=26 and here:
http://fs-uae.net/plugins if you manage to get it compiled.
(If you now use the latest git version of qemu-uae, you also need the latest git version of fs-uae to go with it...)