I'd recommend (and it sure is the consensus around here) always routing everything through master bus and using that as the export source.
That's the best way to make sure you're in control, meaning that some tracks aren't going directly out, missing buses with FX or something like that.
Also, normally people want to have a high quality file of their project, not only a lossy condension. That's why they export as wav, and convert that to MP3. For temporary checks etc. direct MP3 export is ok, obviously.
And to be picky about the terms :o): You save all your automation just like anything else, pressing Ctrl+S.
Exporting is another thing.