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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.

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1) This is a really cool design. I've got all the parts built and the electronics on order, and I'm hyped to get this running for my wife. Thanks for putting in the time to design and upload it. :D

2) That said, its good practice to upload the .stl files in the orientation you designed for them to be printed. It's not always obvious - like with the housing - and keeps you from needing to answer questions like this. It also saves everyone the (admittedly minor) annoyance of having to reorient every single part.
I'm sure you already know this, but if not (or for anyone else reading this who may not know)...its as simple as uploading to Slicer, orienting it the correct way, and hitting "Export .stl" to save over the original file. Next time you open it it will be in the correct orientation.
Just a thought. :-)