I'm confused you want the best quality but you want nero to encode it
for the best quality use tmpgenc and do the header trick
http://forums.afterdawn.com/thread_view.cfm/40078
to really encode movies the right way you need to follow a few guidelines
1. http://divxrepair.sourceforge.net/ remove all bad frames
2. make sure tmpgenc is set up correctly (don't worry about setting you don't have, just the ones you do have )

3. If you want to speed up the encode you can put it on motion estimate search but remember you're giving alittle quality by encoding that way, transversely if you put it on best quality, it takes even longer but you get the very best
hope this helps