I am using Glyphs 2.0.1 (740) and after draw all glyphs and diacritics in Mark section, but when I generate the Basic Latin / Western European the glyphs remain empty. I remember using this and the components of the glyphs + the mark appear inside each glyph. Something has changed at this versions? 
Use the combining accents, not the spacing accents. Rename them by adding a ‘comb’ at the end. Take a look the updated Diacritics tutorial.
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My current font still uses the spacing diacritics from the previous version of Glyphs. Is there a reason to go through the effort of converting to the *comb formalism?
Is it OK if the *comb diacritics are aliases of the spacing ones, or do they need to be improved somehow?
Finally, is there an easy way to generate all the Adobe Latin 3 and Latin 4 glyphs?
You can keep the spacing accents as components. There is nothing wrong with it. Only if you don’t have *comb accents, the accent cloud is not working.
But to convert them takes only a minute. Select all spacing accents in font view, hit cmd+shift+F leave the search field empty and put ‘comb’ in the replaces field.
As I added more language diacritics I have overlapping problems with my current baseline - which are the possible solutions on this issue? I think change baseline height (changing Ascender?) and the other is to keep the baseline and change the diacritics drawings?
Thanks for any advice
Not sure what that means. Can you post a screenshot?