Put both on the first IDE and set the HD with windows as master and the second one as slave. To do this you have to look on the back of the HD and set the jumpers (little clips) to the right setting. It usually says that on a sticker on the HD.
No it does not. As long as the motherboard has the proper connectors for the hard drive you are installing, IDE or SATA, you will not have to replace it. If the connectors are different, then return the hard drive and get one with the proper connection type.
operating system
the hard drive should be set to master...
I would suggest installing windows on one hard drive, then installing ubuntu on the same hard drive. Use the other hard drive for the backups (partition it).
Installing the program to your hard drive
without a hard drive your PC wouldn't work at all. so you must have a hard drive, whether its internal or external...
You normaly only need a srew driver
yes you do.
Defragging the hard drive
yes all hard drives must be reformatted before installing an operating system.
configure the bios settings to auto detect the master hard drive
Installing a second hard drive in your system will have an immediate impact on system performance if your system is memeory bound?