Yeah, I got my Rep2 a month or two ago, and I've definitely found that there's a learning curve.
1) Make sure it's in a temperature-stable area, preferably 70F or higher. Don't blow fans on it or put it near open windows. Temperature gradients inside the build area can lead to warping and delamination.
2) Use the blue painters' tape that comes with the machine, and buy a few rolls to use thereafter. You can re-use the tape until it starts to tear up with use; no reason to replace it with each build. Using the tape aids adhesion to the build plate and helps prevent the first layer from peeling back--a surefire way to ruin your prints.
3) Make sure to design your parts so that there is a large flat area at the bottom. Even if you plan to remove it later, the flat area (known as a 'raft') will aid adhesion. Don't use the Makerware's built-in 'raft' feature, because this doesn't always stick well to the build plate. A single .25mm (i.e. one layer at Medium res) solid chunk at the base of your part will suffice.
4) You'll need a pair of needle-nose pliers near the machine for removing build supports, and a palette knife to separate parts from the build plate. I have a painter's knife that works brilliantly.
5) The extruder can bridge over taps of 2cm or less without much difficulty, so keep that in mind when deciding whether or not to build 'supports' into your print. Supports are indespensible at times, but if you can get away without using them the prints will often be much cleaner. A little planning while still in CAD land is a big help.
6) Be sure to tighten the X and Y motor couplings before you use the machine and frequently thereafter. If your prints are leaning to one side or another or you're seeing unexpected tolerance problems, this is likely the problem: http://www.youtube.com/watch?v=76XaGlyG0Z0
7) Be sure to lubricate the X-pulley frequently by adding grease and then jostling the belt back and forth. The grease quickly gets squeezed out, and a sticky pulley can mess up your prints. If the printer starts squeaking at you, that's probably the issue. http://www.youtube.com/watch?v=NP47vjSZQtA
8) I found that the Makerware 'Medium' quality setting is fast, but quite poor quality. The 'High' quality setting is incredibly slow, but better. My compromise is to keep the quality preset on 'Medium' but crank the thread size down to .1mm (rather than the default .27mm), and up the number of walls to 3. That seems to work beautifully for most prints, and it slices much faster than the 'High' resolution setting.
Good luck!