One way to avoid troubles with various distros that have different sets of config files is to have a /home/shared directory which contains only personal files that can be safely shared between distros (.bashrc, .xinitc, etc.). These files would be linked into the individual home directories, so they can be accessed easily from any of the distros. Any files that are specific to one distro would be "real" files in their respective home directories, where they wouldn't be used by the other distros.
This might sound complicated, and it is somewhat complicated to set up, but as long as the UID is properly set for each user it can actually make modifying your configs much less of a hassle (make a change to .bashrc in one distro and it is also changed for the other distro). As far as plain old data files are concerned (images, downloads, music, etc), I think pixellany has the right idea.