Use of "does" is correct because "side" is singular.

It would not be appropriate to use "which" because it is not a question of choice; we do not know how many sides there are. The fact that there is a Mr A and a Mr B does not imply that there are only 2 sides. The answer could, logically, be, "Mr A represents side 1 and Mr B represents side 99."

It is correct to use "each", or commas, where 2 sides are required to be identified. Without "each", or commas, 'Mr A and Mr B' would be a compound subject.

What side does Mr A and Mr B represent? - Mr A and Mr B are partners who represent one side.

What side does Mr A and Mr B each represent? - Mr A represents one side and Mr B represents another side.

What side does Mr A, and Mr B, represent? - Mr A represents one side and Mr B represents another side.