I have a similar setup,
80Gb primary HDD --> OS
1.5TB Secondary HDD --> Media
Cant remember off hand how I got it working, but I didnt have to edit any config files,
I added yhe second HDD after the install of Linuxmce was completed. Then the orbiter on my Core/Hybrid came up and asked if I want to use the second HDD. If I recall corectly I chose as "FileServer Storage" or something similar.
After this was done I was able to browse to my Core from a WinXP pc and just map it to a network drive.
Im not at home at the moment, but will test it later and post my findings.