I would recommend that you save each version (e.g., draft 1, draft 1 plus comments, draft 2). But work on the latest version (separately saved). It makes it easier to see what you've addressed from the comments etc. Also useful for the supervisors if you are sending it back to them for more feedback afterwards, as they may have forgotten their original comments. I normally put a reply to any comments, e.g., "addressed".
Best
Tudor