File System backup; where does /C drive backup go?

I recently made a backup of my File System (not just my Home directory) to an external HDD and assumed that Wine files on /C would be backed up as well.
On restoring, all files except those on /C are there, nothing from Wine. Where would Simple Backup normally place such files. What must I do in future to ensure that such files do get backed up - in my case most of those in question are CAD drawing files, very time-consuming to replace.