MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
When I bought mine I went through the same thing. I wrote down everything I learned in the following two sections. I haven't updated them lately and I ought to, but they should get you going. Hit me up with any questions you have.
(Detailed Build Guide) https://www.thingiverse.com/thing:2721502
(Detailed Calibration Guide) https://www.thingiverse.com/thing:2722557
Once you've gone through the calibration, you should be able to print some things fairly successfully.