arduino uno embedded into a PC

Dear all
I am new to Arduino I am trying to build a new developing environment so that the arduino board reside internally into a pc.
I have bought the arduino uno and I am trying to connect it internally with this motherboard:
http://doityourselfhtpc.com/2010/08/30/asus-at3iont-i-deluxe-review/

I have 2 questions:

  • is it possible to connect the USB of the arduino internally? The motherboard has 2 usb internal connections but on the arduino I see only the external one.(shuld I just get an internal usb cable?)

  • I would like to keep the other connections(analog and digital) of the arduino board sticking out of the pc box, so that I can us them when need it, what is the best approach?

Many thanks
Nic

Keep your arduino out of the box. And just use usb to talk with it.

Do you want to use shields too? Then inside is almost no option.

What model PC you have in mind (laptop, desktop, server, ...

Be aware not to obstruct the heatflow inside your PC as it is needed for cooling A harddisk bay could be a good place.

Where do you want the IO connectors? back front side other?

Most important, what is your goal , the reason to internalize the Arduino's? There might be other solutions...