First question, what I did was just draw one line through my totals and wrote the new times beneath them very neatly. I put an explanation in the remarks section.
Second, for neatness, yes you can just take the sim time out of the total time and have a simulator section. Word of caution, I think 141 schools count the sim time in the total time so you can meet time requirements for certain certificates. IF that is the case, it may look like you didn't have enough total time to take a check ride.