Unless you do not select the second HDD (the one with the VMs on it) as the installation drive, your VMs should not be affected by the installation.
Please don't mind me asking, but how did you burn the .iso image to the CD (btw. it's a CD image, not DVD)? Did you select "Burn Image" (or similar) in your burning software? You may also want to check the boot order in your system's BIOS.
André