Since I've read the first half of the manual (then had my power supply go out)... I can answer the first part.
The difference between Object mode and Edit mode is that, when you edit something (extrusions are done in edit mode -tab key shortcut-) anything you do is added to that particular object... In other words, if you want to smoothe one part and not the other, create the first one in edit mode, then switch to object mode and create a new object.
you can also duplicate something in edit mode then change it so that its mesh isn't "linked" to the original object. I forgot how to do this exactly, but check out object linking in the manual, it's a lot like virtual inheritance in C++.
A 3rd way to do it is using layers. The layers in blender are selected using that 20-button area in the upper right of the lower navigation area, just above the buttons. You can do use this for making sure only one part of the object is visible at a time, even for rendering. I never read much on it, as I'm not gonna animate in it for a bit.
Hope that helps! Try using another free program (anim8or for example) to add the other stuff and export, might be easier. (unsure on that)
Signed
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