it depends. if you want small form-factor go mini itx. if you want no compromises but still want to keep it small go M-ATX. personally you don't really want to go SLI. dual GPU setups have their headaches on games as it is. i don't think you want it with an expensive card like that.
i would go M-ATX however cause your options are much more open than mini-ITX.
What are you building that will require 2 780Ti's, what is the purpose for this build? Anyway, if your really looking for that much power you might be better of buy both cards and making sure that the motherboard can handle both of them. But more information is really needed on your end.
Thanks for all your comments and I was doing a lot of thinking and I have decided that I want to get mITX because of the power of the 780Ti and how long it may be before I get around to upgrading. If you want to see the mITX build I want check out this: http://pcpartpicker.com/p/2TYkT Thanks again!
Is there a brick and mortar Microcenter near you? If you could, I would recommend a call and see if they could hook you up with any of the promotions they may be running. I happen to bring my friend with me to pick up a hard-drive just at the time he wanted to build a computer and they offered him crazy promotions. Z87 Motherboard and i7 combo saving him around a total of 120 or so with his entire build. It's not even something that was mentioned on PC partspicker.