Flywheel, Bpivk is correct. SME has been designed to work a certain way. Part of its idiot-proofing is to delete changes (at reboot) you make unless you make them in the proper way. That way you get restored to a known, operational configuration after reboot.
You could create a directory in an ibay then mount your data disk as that directory .... but it is possibly overwritten in an upgrade or reboot (maybe, maybe not...I am not sure).
The designed way of sharing data with SME is to use an ibay....copy your stuff across from your data disk to your ibay.
BUT - if disk space is your problem, try what you suggested. Read this first:
http://mirror.contribs.org/smeserver/contribs/mblotwijk/HowToGuides/AddExtraHardDisk.htm#homedirDon't format your data disk...it is already formatted and full of data. Use fstab to automount it to your already existing ibay directory. (it might even be possible to use the "files" Directory of the ibay as the mount point. [***if your data disk uses rieserfs, then you may have a problem....I think SME uses EXT2/3 and not reiser***]
If it works, test it after a reboot to see if it keeps on working.
After all, if it works, you are ahead. If it doesn't, you should still have your data disk intact.
However, the best way to do this is to get two large disks of equal size (identical disks is best) and load SME and your data and let software raid handle redundancy. You can even implement backup to a USB disk or to a Windows workstation or whatever.
Good luck
Cheers
Ian