Well I enjoy trying to be very clear (bar a few spelling mistakes at times!)
So here is the answer
Install the drive that you want to use in the computer (note: this may be both drives, first one plugged into IDE0 and the other one plugged into IDE1, on the motherboard)
Boot from the Windows CD
Allow all the initial Windows drivers to load
Reading the prompts on the screen you will see information on currently installed Partitions. At this stage (again following the screen prompts) remove the Partition(s) )
Continue setting up Windows (ie you do not need to manually create a new partition)
When Windows is finally installed, you need to locate all your Manufacture drivers (actually you could do this first, and save all the drivers to a CD)
That's about it, nothing else to say (except make sure to do all Windows security updates, and get an Antivirus, like Avira free Antivirus)