I found a link that talks about how to do this.
http://lists.forgerock.org/pipermail/opendj/2011-February/000069.html
A copy and paste from there is as follows:
It is possible to separate the installation directory (i.e. scripts,
libraries, etc) from the instance directory (i.e. configuration, db files,
logs, etc).
The easiest way to do this that I know if is to modify the contents of
the instance.loc file so that it contains the path "/var/opt/opendj". You
should then copy the following directories over from your install directory
except for the core schema files:
cd
echo "/var/opt/opendj" > instance.loc
cp -r changelogDb config locks logs db /var/opt/opendj
rm /var/opt/opendj/config/schema/*.ldif
You should then be able to do the following once you've configured the
server according to your needs (e.g. the LDAP port):
cd /var/opt/opendj
/bin/start-ds
If anybody else has anything else to say about this topic I am all ears.