Yes you can do that, but you need to save out different g-code so the printer knows which nozzle to use. I use simplify 3d and have profiles for each nozzle, and just save "left" and "right" versions of the file.
Dual printing works by telling your slicer that you're using a single extruder printer and then setting the printer to "dual" in the LCD menu. You just have to make sure that your objects aren't wider than the distance between the nozzles, which is limiting. Still it's awesome to print 2 small or thin objects as quickly as you can print 1.