The C: drive in Windows is most likely referred to in Linux as sda, where the first (and possibly only) partition on that drive would be sda1. If you have a 2nd fixed disk drive, normally D: in Windows, it would be called sdb.
When you run the Ubuntu install, it will normally run a live version from the CD or USB, with an option to install permanently. You can use disk tools to be sure that your Windows disk is indeed sda1. Then, when you install, I believe there will be a choice to install onto sda, with an option to erase everything and reformat the drive to ext4, the default file system type. This is what you want to choose. This will not do anything to the 2nd drive, or any other drives. Just be sure the disk you choose is the one with Windows on it; it should be pretty clear with the installer, as it is a GUI representation of your disk, and shows what is currently on it.