Where should my parents sit during the ceremony?

I believe that everyone should be reminded that is your day and about you and your fiance. So, everyone should put their differences aside and focus on that. The ceremony is not extremely long. If you have a reception I wouldn't sit them at the same table, however for the ceremony I believe they can keep in mind that it is about you and your fiance and put their differences aside. I feel like you can put your mother and father on the same row but just put others between them to distant them.

Any chance asking your mom to just be polite and ignore your dad during the ceremony would fly? If she's really concerned about traditional seating and sides above all else, she's going to have to deal with some proximity to your dad. There really isn't much interaction during wedding ceremonies, and all the activity is focused on the couple. Plus parents are usually escorted down the aisle at the start of the ceremony, so it's not like they'd be sitting there waiting and forced to make small talk. If she's the only one making a fuss about not sitting near someone, it does serve to reason that she should be the one in an alternative spot, which you've given her an option for. Other than that, I'd say maybe stick a family member (or a few) between them that they both get along with.