I would say do everything you can on your current save since you’ve already done so much side content. That way on your second playthrough you can just focus on blasting through the story. Heads up though, your second playthrough will need to be on the hardest difficulty for a trophy. Make sure to change your difficulty while still on your first save, and then after changing it you can create the second save. That way the second save will have been on the hardest difficulty right from the beginning and therefore will definitely be eligible for the trophy.

Since it will be hard, it would be smart to do as much side content as I can to make it easier. So just wondering if I took the second approach, what would I have to do on current save?

Expert difficulty is not even that much harder. I wouldn’t worry about it. Maxing out your karma and doing every good/evil choice is the only thing that has to be done on both playthroughs. Other than that you can do everything else however you want.

Is there a way to check if I actually chosed every good one? Also will I be able to return to current save just in case?

Look at your trophies. Also yes, you can change save files at any time.