Re: Board Level Design
There's a lot of difference between FPGA designs and board level designs. As neerajs says, Signal Integrity is a very important domain which never comes into picture during FPGA designs.
Are you planning to concentrate on the front end design or the PCB design? In either case I recommend you to start with OrCAD to start with. I recommend you to study "High speed Digital design, a handbook of black magic" by Howard W. Johnson and Martin Grahan by Prentice Hall if you want to learn about SI.
Best of luck,
it_boy