Yes, you need to save the file as *.ncf
Is this a TSU500 model BTW? And yes, you got it on the last part. Everytime you save in NeoEdit, the software creates the OVERVIEW device pages. By making your own as a Device, you can then run MAcro's(Links)
and such off the device Overview page, also you can hide devices, since there will not be a link to them if you don't put one in.

And yes, if you re-DL the file back to NeoEdit, chanses are good that the Device you had moved to the top of the device tree will be GONE! That is why it is important to save the file as a different one.

So basicly, layout you ncf as you want, but just test everyting off your own device startup page that you plan to use. When everything looks good, move it to the top(startup) and give it a go. It isn't that hard to go back and change something if need be.

-steve