"Which side DO Mr A and Mr B represent?"

or
"Which side DOES Mr A and Mr B EACH represent?"

The word EACH imperatively refers to a subject in singular.

It is true that the subject is singular, but that does not dictate whether the auxiliary verb, 'do', should be plural or singular.

The verb in the sentence is 'represent". The OBJECT, that which is created, affected or altered by the action of the verb, is 'side'. Side is used in the singular, therefore the auxiliary verb must also be singular.

Also, once again, it IS NOT a question of choice and therefore 'what' should be used.

Now, what did you have to say, the other day, about real English teachers, Mr H?