For l4d2, the mapping will simply be an addition to the l4d tools, when it is ready, but for now, you can make it just the same as l4d2 (if you have l4d, l4d2, and l4d authoring tools) with these tuts.
No the .fgd does not effect the engine just hammer. For example I use a Team Fortress two fdg that adds some entities and changes the info_player_start to a different model but, for example, if I replicated a valve map and play it on my server there will be no difference between the two maps and no one would notice whether or not it was made on a custom .fgd or the one valve used.
I dont have L4D1, and even if I did have it i wouldn't mess up with, I would just wait. I dont know for sure if it is compatible or anything. Anyone knows how to get a beta for the sdk tools? There is nothing on the properties of the game or steam XD