There are two separate plugins. One für webmail, one for phpmyadmin. Both request an installed version of the corresponding software in /var/www i.e. the webmail program has to be reachable through /var/www/webmail and the phpmyadmin through /var/www/phpmyadmin. Whether these are symlinks to another location (e.g. /usr/share/squirrelmail or /etc/usr/roundcube) or really installed under /var/www doesn't matter.