I don't know if you got your answer or not. But by default splunk is installed into /opt so if you installed in lets say /mnt/XX and you wish to update it, simply issue the following command:
rpm -Uvh splunk-6.0.2-196940-linux-2.6-x86_64.rpm --relocate /opt=/mnt/XX/
(The relocate part tells splunk to apply the update to /mnt/XX/ instead of /opt)
You can alose use the relocate part of the command to change the default install directory.