The single object is actually made of two separate, interwoven STL files that are placed at the same location on the print bed. Look for the candy cane sample file on the CD that came with the printer. It's just creative slicing and dicing with the modeling software.
For example, you could cut away all the green parts so you're only left with what should be printed in red, then Save As Flower1. Then undo (or go back to the original file), delete the red parts so you're left with only the green parts, and Save As Flower2. Place both STL files and make sure they're in the same XY location with the proper Z offsets (if they don't both touch the bed).
Thank you both for your responses. Bought the printer and ran my first prints off last night including a successful multicolor print. Very quickly realized the stock Mac software is nearly unusable and purchased Simplify3D - looking forward to a lot more printing over the weekend. Very pleased with this purchase already and looking forward to hacking into this thing once I have a little experience under my belt.
I would be very interested (and I'd appreciate it a lot) if you'd post your experiences with Simplify3D. I'm very interested in this especially if it allows "point and select" color changing on individual pieces. My interest is in printing two parts but one of each color - similar to how the XYZ software worked when I first got my XYZ. Hopefully that makes sense!
I saw a video where the person was explaining all the features and I THOUGHT I saw him do something like what I'm describing..