you select the nozzle from the main screen.
Click on the moel to select it then click on the bottom left option - that will let you set a particular nozzle for a particular model.
Haven't used makerware for awhile so I can't remember what the button is called. But it's bottom left of the model setup window.
The model also changes colour depending on which nozzle has been allocated to it.As far

as all your other questions go - BUY A BOOK :-)
I recommend this one: http://www.amazon.com/Practical-3D-P...printing+brian
read it from cover to cover. ANd it'll answer about 90% of the questions you obvously can't be arsed to google :-)