I am fairly new to building computers, and I am starting out with the mother board. What are the parts I need to build a motherboard? Also, how can you reprogram your BIOS?
If you're new to it you can't design your own PC's motherboard. Despite their low cost motherboards are pretty advanced electronics. A common EDA tool like Eagle is not fit for the job, where you need to take transmission lines, matched impedances and matched trace lengths into account.
A typical PC motherboard may have more than 10 layers. Having made one will cost you more than a PC from the shop around the corner. So you want to make it right first time. So you want simulation tools. Cost: several 10k, up to 100k dollars.
You can't prototype a > 100 MHz PC motherboard on a breadboard, it simply won't work. Besides, all the required components are SMD, many BGA.
How to build a motherboard
What are the parts I need to build a motherboard?
If you are planning of integrating at circuital component level than I can't help.Its something where you really need infrastructure and precision to integrate such things.
If its about assembling motherboard components then you can refer here
Also, how can you reprogram your BIOS?
If your computer is some new model from previous 2-3 year release, then believe me you are going to do a dangerous job.Its not suggested to flash your bios, because your manufacturer writes many routine specific to your computer assembly.
However best solution is to override your bios settings, as many OS vendors do.There is a concept of Unified Extensible Firmware Interface where you can add functionality to your present bios.However many simple necessity like USB booting(not supported in previous computers) are tackled by linux grub easily.You can try your hands by modifying grub as well.