Interfacing DDR LVDS Outputs to uC

The first thing you need to do is stop throwing around alphabet soup and start thinking about what you're saying. Then you can translate your request and see what you need to learn.

So you have some sort of analog sensor/signal that you're interfacing with a 14 bit Analog to Digital Converter, then you want to transmit that digital double data rate stream using low voltage differential signaling which you want to interface with the analog front end of your Atmel μComputer which you suspect can be set up in differential mode.

Second, are you an electrical engineering student, a programmer, a computer scientist, or all three? As an electrical engineer can you tell if the ADC outputs a parallel or serial data stream, whether your μC front end accepts your chosen data rate, and if it accepts your signal levels. As a computer scientist can you tell if the baud rates are consistent, that the signalling protocols are all met, and that the message gets received as transmitted. As a computer programmer can you tell how you are going to implement the ISO 7 layer model, how you're going to build your stack, and make sure the data gets where it's supposed to go once it's inside your μComputer.

Third, I sure hope you took good notes in all those boring classes that you were supposed to sit through as an undergraduate student, you're going to need all that info to do your project.