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.
Better still, get a pass through bowden connector, increase (or drill out) filament path to 4 mm, and let the PTFE-tubing go all the way to the gears. Less friction than drilled through plastic; also makes for fewer junctions in which filament can get stuck. I made this yesterday: https://www.dropbox.com/s/jinvs396ew5yh9g/bowden.jpg?dl=0
(I'm still waiting for my MK8 drive gear, which should arrive tomorrow.)
Sort of like what the E3D people suggests you do: http://e3d-online.com/index.php?route=extras/blog/getblog&blog_id=21 (and more specifically http://e3d-online.com/image/data/v6/626%20done%204web.jpg)