Since you've installed to both partitions now, you should reformat the entire disk and start over.
From what you explained earlier, your system came with a recovery partition. That partition was destroyed when you installed your operating system onto that particular drive which removed what WAS there and replaced it with your system, thus becoming the system drive. This drive was meant to be your system's safety net from which you could recover it to it's factory condition. That I'm afraid we cannot get back for you but we can get you reinstalled, then once you have the system back the way you want it, you can install some freeware that I'll point to later, and you can use THAT as your safety netting. What the software will do for you is to create an image of your system much like system restore does. This however, can be stored on removable media so that you can, if needed, use it to restore your entire system, updates, software, and all, just as it was when you took the snapshot of the system's condition. More on that when you return.
For now, you should insert the installation CD. Remove everything from the back of the computer except of course, for your keyboard, monitor and mouse.
Reboot the computer making sure first that your BIOS is set to allow the system to boot from your CD ROM drive. Since you've already done this, I assume you need no other instruction on that.
During the installation process you will be able to select which partition you want to install to. It's at this point you should highlight the other partition and select t "Delete" it leaving nothing but the entire disk space available for installation. Make sure you take advantage of the option to format the entire disk...and don't go the quick route either. It will take a few minutes but it's worth your time. Be certain you choose NTFS as the file structure.
Once the format is complete, begin your installation. Allow windows to do the rebooting...you need to do nothing else until it's complete.
Once you've completed the reformat and reinstall, only then should you reconnect everything else to the back of your computer. Make your FIRST online visit be the Windows Update site and install ALL the updates it finds. Not just what you may THINK you need...please allow Microsoft to install all of them. You can always remove later whatever it is you think you don't need.
After you've installed all of those updates, next you should visit THIS web site only and I'll give you more instruction as to any third party security software that you may need. Good luck! I'll be on here intermittently today and later on this evening.