I don't think I qualify as an expert, but I can try tackling some questions...
Start out by looking over the Makerbot wiki
. We have a Cupcake with a Mk5 extruder. You'll also need a copy of ReplicatorG
(I think it's installed on one of the lab computers, but it's good to have on your own machine as well).
You should know right up front that the Makerbot takes some practice before you can get good prints off of it. You might want to start out with one of the calibration sets
off of Thingiverse
, they'll help you get the machine dialed in.