I would recommend installing atmail in /usr/share/atmail then change the squirrelmail directory to squirrelmail.backup or whatever you want. Then change the directory of atmail to squirrelmail and the symlink would not have to be changed. If you want all the domains to automatically have the subdirectory /webmail just add this line to your /etc/apache2/apache2.conf and change the path to your correct atmail path!
Alias /webmail /usr/share/*directory to atmail*
then restart apache and all domains automatically have the subdirectory /webmail ! Be aware that this does not automatically create the directory, its more like a symlink to all the domains .. they will all use the same files located in /usr/share/*directory to atmail* !
Depending on which path you chose to use you might have to change permissions to allow the access to the files.
Have Fun, hope this helps