After starting Arma, go to the 'mods' tab and create and save a preset for your 506th mods. then, unload all or whatever subset of mods ( such as 506 TFAR), select the STEAM sourced TFAR from the list of mods and add it to your new mod load out. Save the mod loadout Generic or whatever. You will have to remember to switch to your 506th mod preset and vice versa before you log into 506 servers.
Alternately, Go to your library locate Arma3 right click it and in the list it says "create desktop shortcut" and append the mod list you want to the shortcut "-mod=@mod_name;@mod_name2" or whatever.
