The two drives should be different model numbers, for instance, I have to WD 80Gb HDs. One is IDE the other is SATA.. the IDE is the model number ending in JB and the sata is the same, but it ends in JD.. So look for something like that to clue you in to which is which..
Also, make sure the drive that is set to master on the master on the cable, and the same with the slave.. sometimes if the BIOS is trying to auto detect, and the jumper/cable orientation is wrong it gets messy.
As far as "seeing" the hard drive, is it initialized in windows?
(right click My Computer->manage-> Disk Management (at the bottom).. if the drive is there, right click on it and select Mark Partition as Active.)
That might solve it.. Sometimes you have to initialize the drive for MS to actually let you use it.