Haha, yes, manuals can be useful sometimes :rolleyes:
You can print multiple models by selecting them in the Process Settings:
Process Settings -> Select Models (button on bottom of process settings screen)
http://i.imgur.com/LuXTExq.png
This way you can use different processes for different parts/models.
If you have multiple processes then it will prompt the following when you want to print:
http://i.imgur.com/e2hPqfC.png
And then you can either do sequential printing with clearance height (the height it will build 1 object before switch to the next) or continious printing (most used one due to dual extruders & bars being in the way when doing sequential printing)
Good luck!
EDIT: I was using multiple parts / processes here to do some testing with different variables for optimal printing.
EDIT2: Also; always check the print in the 'Prepared Print' windows before exporting because what you see is what you get! If you only see one part; then you'll only get one part - so go back and change your settings and Prepare your Print again! :)
Makerware works perfect too! The only reason I switched to Simplify3D is for the custom supports & ability to add different processes (and doing layer-based settings.. and some other stuff ... :o)
If you have any questions about Makerware then we can probably help you too, else try the Makerbot subforum on this board!
Good luck to you too!