Once you've done it a few times, it's simple. If you haven't done it before, I recommend reading up on how to do it or have a friend that has done it before be with you.
Basically, you need to make sure you have all the necessary hardware drivers ahead of time. You also need the OS install disk. Detatch all drives except the one you will be putting the OS on. Set the bios to boot from cd/dvd first. Boot from the install disk and follow the instructions. After the OS and drivers are installed, you can switch the bios to boot from the drive. Once you are sure it's working, attatch any remaining drives.
Ubuntu and Fedora are operating systems based on the Linux kernel. There are many operating systems that use the Linux kernel (sometimes these are called "Linux distros"). I recommend either Fedora 17 or Ubuntu 12.04.