Please understand that the information that you have requested is very complex and would need to be covered in several college courses, if not an entire curriculum. Designing a motherboard would require an Electrical Engineering degree and programming the many types of chips would require many different Computer Science courses, probably at the graduate student level.
I doubt that one person has ever designed a motherboard by themselves, not to mention programming all the firmware and device drivers needed for the chips. Beyond that is the actual fabrication of the board, and the equipment and resources to do that are beyond what one person could pay for, as well as accomplish.
I recommend that you get some of your fellow students together to assist you in this, as well as professors, and I wish you good luck!!
The simpler the device the easier it is to design a board.
Radio Shack sells a kit that will allow to to lay out very simple boards for small projects. (single or duel sided) http://www.eham.net/articles/20120
The more complex you get, the more places you have to get in to trouble in a design.
High speed signals are very sensitive, You can have two identical wire traces, running parallel on a circuit, but have different impedances in them because of capacitance and inductance for other layers of the board which may pass under one trace but not the other.
Many computer boards have over 7 layers of traces, one top of the next that all have to be considered when doing design.
If you looking for code development, their are many embedded test kits on the market to allow you to do basic embedded circuit designs.
My recommendation is if you have something specific in mind to build, first research it on line and see if someone else has already made something similar that you may be able to modify to suit your purpose. It is amazing how many general purpose modules and development kits are out that that can be interconnected to make some really cool stuff.
As far as languages, If your building with a small micro controller, you may program it directly in machine code.
Computer BIOS is mostly done in some flavor of C.
Applications to run on the computer, C, Java, Python.
You may also want to GOOGLE the USB specification ot the PCIe specification. These define how a device is expected to work and respond.
Good Luck at good old SomeCollege
Ya know Doc, I guess I was reading more into his post then was there, you are correct about circuit board kits that are available, or going so far as etching your own. I've always wondered how the multi-layer boards like you mention are soldered, is that done by some immersion technique?
Since you seem to know something about this, I'll ask you. I've been trying to solder some surface mount resistors on a board and am having some problems. Do you think my old Weller soldering gun with the trigger-activated heating, neon light, and the copper, bent coat hanger style tip is the problem?
Worked fine for my Dad when he was soldering up some 12AX7's.
In truth, I have never been to the finial factory where they assemble to boards. The use "wave solder" (http://en.wikipedia.org/wiki/Wave_soldering) for most of the components but one of these days I would like to go see how that works. (I keep visualizing a water fall or breaking ocean wave washing all the components off the board). Some components due to size or mounting requirements are hand mounted. The boards are then opticly scanned and each component checked for solder bridging or other soldering defects before being sent to the first of several sets of tests.
As for your old Weller, I would have to guess the problem is about a arm's lenght from the tip or the iron
Of course if you can still see the surface mount resistors your doing bettter then I am. They mostliy look like pepper specks to me
Working under a microscope is required for almost everything today. I use to be able to replace parts with a bench magnify glass, but these 402 resistors are too small for that now and if I need to replace a really fine pitch components, I send out to a rework tech....
... the times they are a' change'n...
as one guy once sang... and have they ever...
My father was an engineer during the genesis of television in the '40's and '50's, worked for Scott Radio and Sentinel among others. Retired when Admiral went out of business, and actually received compensation from the government because it was recognized our friends in Japan took over the TV industry by "dumping" their products on our shores (hey, we bought 'em.) We had an old TV in their home, B & W of course and only covered the VHF band, maxed out at Channel 13. A true relic, my parents put it in the garbage... I about expired... I wanted that baby for an antique. My dad had soldering irons that would put waffle irons to shame, he would not believe surface mount stuff these days. I'd love to see a fab plant for motherboards, not to mention the CPU factory.
Hey, I get yer arms length right here... not to mention solder balls...