Sorry for the double post.
I've done the above method of separate game folders for separate servers.
Now on the ACE server, with signatures enabled, upon joining the game I get this error
The server keys for carraigdubh and sg_ira are in both the modifications "Keys" folder and the arma 2 root folder Key's section, however the signatures are named "sg.bikey" instead of "sg_ira.bikey" so should that matter or not?
Warning Message: Files "E:\ArmA\@FOG\addons\carraigdubh.pbo", "E:\ArmA\@FOG\addons\carraigdubh_obj.pbo", "E:\ArmA\@FOG\addons\sg_ira.pbo" are not signed by a key accepted by this server. To play on this server, remove listed files or install additional accepted keys.