As one of the early Bitcoin FPGA devs, I say go for it! You won't swamp the network rate for a couple of reasons any time soon. FPGAs are generally slower than GPUs, and relatively expensive -- fewer people have them (think about the average gamer with a strong GPU, vs. the average electronics hobbyist with an FPGA).

It's only power efficiency where FPGAs win in the long run, and this requires wider adoption. In the case of Bitcoin, FPGA miners paved the way to ASICs, and it was only those that really took GPUs out of the business. At the moment, Blakecoin (and its mergemine coins) have had FPGA miners for some time already, but GPU mining is still somewhat profitable. Of course, the low power consumption is a personal gain for any miner

As for the tech specs -- in any coin, hash.h tells you how the algos are chained up, in this case it's 640-bit data -> Skein -> 512-bit hash -> SHA2 -> final 256-bit hash.

Do have a look at other FPGA projects like the Blakecoin one for examples. Also, I cannot help but link my own -- the Python mining script might still serve as a simple example on how everything works together.