Yes - you definitely need to have the 2.40 version of mcc18. Newer versions are incompatible with the IFI-provided libraries (plus they cost real money after the trial period
I think if you poke around in the Eclipse project properties box, you'll eventually figure out how and where to put things. I'm still trying to figure out the best organization for my team (FRC, using Vex for prototyping), so maybe when I settle that I'll try to post my findings (and project files) here.