I'm coming in kinda late on your issues here, and I am in a hurry, but I will try to give you some answers that might make sense
First off, do you want to install the original disk or with the one you recently purchased? I am guessing the recent one is more up to date (contains SP1 or SP2). You have already installed the new one, did you 'activate' this version? (that is the last step, and you activate the version by being on the internet and connecting to MS to get the version activated)
If you have not activated, then perhaps it would be best to use the original and keep the new one for later, perhaps a different machine???
Anyway, with either disk, just put the disk in the cd tray, reboot, and the computer should boot to the disk (you will have to hit a key when prompted early on to boot to the cd). Start the install process by hitting ENTER when prompted. When you see the choices of which partition to you want to install to, you must delete the existing partitions. Read the prompts. Then when partitions are deleted you must create a new partition to install Windows to. You will have the choice of sizing this partition. You can make it your entire hard drive, or you can make any size you wish. This will become your C: drive.
Also, you always have the option of formatting your hard drive via the Recovery Console. More info HERE
Gotta run, hope this helped???