It is actually better normally to put the LFS viewer in the S2Alpha folder, because then the viewer just views the skins folder and you wont have to drag skins back n forth while skinning. You just save the skin and start up the viewer.
But yea, if the abc file is different, it needs a place of its own I'm afraid. But once the viewer gets updated with the newest abc, it's going back to where it was for me.