I guess a big issue would be if you had werewolves which are forcibly changed into wolves whenever there is a full moon. If that were the case you'd have to figure out some kind of system for it. If not, and if the two moons don't have any significant impact on the story (messing with tides), then having more of them won't be all that similar from having trees with blue leafs or glowing mushrooms or crickets who play really small saxophones instead of just chirping.
It'll just be a bit of flavor.
That would depend. In KenzerCo's Kingdoms of Kalamar setting, there are no less than 7 moons. Lycanthropes in this setting set their internal clock, so to speak, on one of the moons, not all of them.
As for their influence on the world as a whole, you could use their gravitational effects on the world for some very funky weather or you can use them as scenery. Another story element I have regularly seen is that one of some of the moons had been linked to supernatural effects, waxing and waning of evil, etc...
So far my 2 cents.
Kn'Trac