mflammia
PLEASE READ THE MANUAL, and please review all menu choices and possibilities that are in server manager, you will learn a lot.
In server manager, you can configure the main domain to point to an ibay, I think it is in the Domains panel, too easy.
As far as moving Joomla from /opt to an ibay ie /home/e-smith/files/ibays/ibayname is concerned, that is also relatively easy but requires command line usage.
I'm sure it has been posted in these forums a few years ago, so search had to find it.
In brief do the following:
Move all the files and folders in /opt/joomla to /home/e-smith/files/ibays/joomla2
It's easy to use the Move function in midnight commander (type mc at command prompt), whatever method you use, make sure the file permissions and ownership do not change, or alternatively use tar to pack and unpack to the new location (also keeps permissions & ownership of files unchanged).
Then change the configuration files to point to the ibay name location ie joomla2, these conf files are in the main directory of your joomla install (or thereabouts), I'd have to look to be exactly sure.
You will also need to ensure that the config files point at the correct mysql database, although if the database name does not change then it should already be OK.
One thing to be careful of is if you reinstall joomla with the contrib to /opt, then a new mysql database will be created which will overwrite your existing database (which is not desirable), so in my opinion it's better to change the mysql joomla database name to something else (eg joomla2) and also change the ibay name to something else other than joomla (eg joomla2), then reflect these changes in the joomla configuration files. As far as I recall these configuration files are not templated, so edit them directly (doing so very carefully). Make a copy before you change any files.
Review the files first, it should be obvious which settings need "correction".
If you do change the database name, then you will also have to reissue the grant command in mysl to give permission to users to access the database, this has also been posted here before, and take al look at the Mysql Howto.