First, let's check for a common misunderstanding on these forums: are these two new drives IDE drives (not SATA)? IDE drives have a data cable from the mobo port about 2" wide with three 40-pin connectors (actually, they are female with 40 holes but one blocked off) - one on each end and one near the middle. If you really do have IDE drives, we'll proceed with how to set them. BUT if you have SATA drives with smaller 7-pin data ribbons connecting each drive individually to mobo SATA ports you have made a big mistake! On SATA units there is no such thing as Master and Slave, and you just might have set jumpers so wrong that you have disabled a drive! So, IF your dives are NOT IDE, lets us know and we can advise how to fix it.
OK, let's proceed assuming you really do have 2 new IDE drives connected sharing ONE 2"-wide ribbon cable from a single mobo port.The jumpers on the drives each need to be set differently - one to Master, one to Slave. On some drives they make a difference between Master with No Slave, and Master with Slave Present. Now for the cable connection. You should plug the END connector into the Master device, and the Middle into the Slave. In each case, make sure you got the connector turned the right way. Because of the blanked-off hole it is almost impossible to do this wrong, but check anyway. On the ribbon cable one edge will have a red stripe. That is the #1 wire and pin. At the mobo end, look closely at the label printed on the mobo next to the port connector. There will be an indicator for which end is #1. Ensure the BLUE connector on the cable end is plugged in here so that the red edge is at the #1 pin end. At each HDD unit there also will be a label on the case telling you which end of its data connector has the #1 pin, and the red stripe of the cable goes here. The END connector for the Master normally is Black, and the middle is Grey.
Now, you indicate you believe the OS was installed on the Slave unit by mistake. No problem to fix - we just set things so that the HDD that already has the OS installed on it becomes the Master of the channel. In fact, to be sure it all gets done right, I suggest you disconnect the one you believe is the Master that does NOT have the OS on it. Then you move the jumper on the "Slave" to make it the Master, connect it to the END (Black) cable connector, and boot into BIOS Setup. Ensure that the Boot Priority Sequence uses that particular HDD unit (probably second choice after the optical drive) , Save and Exit to boot from it. If this works you have confirmed that the one drive now connected really does have the OS installed on it, and you have made it the port Master. Shut down, adjust the jumper on the other drive to make it a Slave, and connect it to the middle (Grey) connector. Boot into BIOS Setup again, check that both IDE devices are being detected, and ensure that the Boot Priority Sequence does not try to boot from this added drive as a third choice. When you Exit the machine should boot just fine.
HOWEVER, you still probably will NOT see your second drive. WHY? Well, ANY new empty HDD unit needs to have two operations done on it before an OS can use it - Create one or more Partitions on it, and Format them. This sequence WAS done by the Win XP Install process for the first drive unit so that it could be used, but you have not done it yet for the second unit. To do that you can use Windows' built-in tool Disk Management, or you can use a utility for Initializing or Preparing a new HDD available as a free download from the website of your HDD manufacturer.
To use Disk Manager for this job, click on Start at bottom left and in the menu RIGHT-click on My Computer and choose "Manage" from the mini-menu to open a new window. On its left click to expand "Storage" if necessary and choose "Disk Management". This will open two panes on the right, each of them scrolling to reveal their whole contents. The upper one shows you only the devices Windows already knows how to use. The lower one also shows you the hardware Windows can see, including some devices Windows does not yet understand. Each device is represented by a large horizontal block. On its left end is a smaller label block with things like "DISK_0", a size, and a few other bits of info. To the right will be one or more large sub-blocks representing Partitions already defined. Each of these will have a letter name like your C: drive, its size and File System, and a bit more. If there is some space not yet assigned to a Partition, it will be a block further to the right called "Unallocated Space". The main block representing your optical drive will not have all this stuff because you cannot define a Partition on such a device. Now, your new disk should be here with no letter name and no info beyond its basic label on the left end. RIGHT-click on its Unallocated Space and, from the menu, choose to Create a Partition on the drive. You'll have a choice of how big it should be and most likely want to use all the drive in one volume. (You can use only part of the space. If you do, when you are finished come back here and find the remainder shown as "Unallocated Space". You can create a second Partition or more in it if you want.) For this first Partition, make it the Primary or Active Partition, and NOT bootable because this drive is for data only - you already have a boot drive. When all the choices are made, go ahead with the Partition operation.
When that is done, come back to this new Partition and RIGHT-click again and choose to Format it. Choose the NTFS File System option. A Quick Format will do the job in 5 to 15 minutes. A Full Format will do a Quick Format, then go though every sector of the drive and test it, marking off any faulty ones (very rare) so they won't be used. Full Format takes many hours!
SPECIAL NOTE: In some versions of Windows when you first right-click on the Unallocated Space and choose to Create a Partition, it pops up a Wizard that combines both Partition and Format into one operation. So watch carefully as you choose settings. If you find options for File System and Quick or Full Format in the same place as the Partition options, make sure to set those as you wish. Then when the job is done you do NOT need to go back and Format it - that part was already done.
When you are done, exit out of Disk Management, reboot and your newly prepared hard drive should show up in My Computer as an empty unit ready for use.
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