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If your HDs are IDE or EIDE, Set the windows drive as the master and the linux drive as the slave. Then run one of those live CDs to make sure linux recognizes both drives.
The partition program that comes with Ubuntu is pretty easy to use.
For a while there were some problems with writing to NTFS disks in linux. So I recommend putting a small FAT32 partition on the second drive to transfer files between windows and linux.
I haven't tried this with SATA HDs yet.
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