I found this to be a good read for beginners getting into 3D Printing. It covers the Replicator 2 but also has lots of good information about 3D printing in general. The software portions of the article are a little out dated so refer to MakerBot's official guides for the most up to date software info.

Zero_to_Hero_Rep2_Guide_DigiFabLab_2013-04-06.pdf