To me it seems there is still an active partition on that disk then. What operating system are we talking about. Windows XP?
This is a tricky one, since most Compaq systems also put some BIOS/SETUP information on some hidden partition on the original system drive. Make sure you have a good backup of all your data and have working restore discs ready.
Try disconnecting that drive completely (power and cable) and boot your system. If it boots ok and you got all your data in the correct place then you first are sure that the current connected single disk is the operating system disk you want. If it does not boot at all, there is no active boot parition on this harddisk.
Next disconnect this disk and reconnect the original harddisk. Do not boot it, but low level format it. This will remove any partition there might be on it, it will destroy everything! Google for tools that can do this for you. Remember that a low level format is not the same as a normal windows format.
Make absolutely sure you do not need the data and/or any (hidden) partitions on that disk before you low level format it!
After all is done, connect both disks on your system. Because the old disk is now completely empty, it should boot at your 2nd disk, since it has an active partition on it.