Yesterday i made a Script to Install and play FarCry, i have a DVD.
The script can you found here:
I dont know, if it will work with cd, but i think you have only to change the Cds in the Drive.
Only if it fails, try to get images from your 3cds:
dd if=/dev/cdrom of=/path/to/image.img
Then mount it:
mount /path/to/image1.img /media/cd1 -o loop
Then register all /media/cd* to your wine, at winecfg -> drives -> Add -> Select drive number and path to the cds, select advance and change automated to cd