I am in the same situation daily. Instead of using mysqld_multi, what works OK for me is installing each MySQL copy to a separate tree, then running mkdir -p data etc var/run var/log/mysql
and copying-fixing paths in a skeleton my.cnf:
[mysqld]
basedir=/home/laurynas/usr/opt/mysql-5.5.12
log-error=/home/laurynas/usr/opt/mysql-5.5.12/var/log/mysql/error.log
socket=/home/laurynas/usr/opt/mysql-5.5.12/var/run/mysqld.sock
datadir=/home/laurynas/usr/opt/mysql-5.5.12/data
[mysqld_safe]
socket=/home/laurynas/usr/opt/mysql-5.5.12/var/run/mysqld.sock
[client]
socket=/home/laurynas/usr/opt/mysql-5.5.12/var/run/mysqld.sock
and finally running scripts/mysql_install_db
. If several servers need to be running at once, then I throw in skip-networking
or assign different TCP port too.