Sorry but I don't understand your question.
The /installation directory is the official Joomla directory.
If Joomla Pack use this directory name for their stuff, contact their support to ask them to use another name.
If you want to restore a website using Joomla Pack and including the PHP code as a slave site, this can not work.
I remember you that with JMS, all the files and folders are shared between the website.
You don't have to restore the PHP files and folders as they are already present.
That does not make sense to restore the PHP file and folder.
Only the DB could be restored if you do not replace the master website DB.
Joomla Pack is not accurate and has also other problem when it backup the Symbolic Link and when it will backup the future JMS 1.2.x DB that will contain MySQL sharing tables.
See other post
/forum?func=view&id=976&catid=3#976
For an accurate DB backup, you can use the PHPMyAdmin tool and its export function.
For an accurate backup of the files and folders on Unix platform, you can use a "tar -cvf" command.