I normaly just dump everhting in the main runtime. I like using the the Sub folders to organize everthing by character and creator...but that is just me. This was not a problem in poser 5 or 6 but in 7 you need to do a back up before an uninstall. with 5 and 6 you didn't need to bother as custom content was not touched by an uninstall. Still not a huge problem as long as you know you need to do it.