Alot, diet, behavior, anatomy are all different. To start the sugar glider is a marsupial and the flying squirrel is a rodent. The sugar glider eats a completely different diet than a flying squirrel, which includes honey, eggs, pollen and other such things. Sugar gliders are commonly more social than flying squirrels because they are colony animals.
You will see a visible difference between the two. The flying squirrel has a much shorter tail that is somewhat flat in appearance. Also the flying squirrel is colored more like the squirrel in the tree across the street, while sugar gliders have facial and body markings. I have only seen one color of flying squirrel, and it was brown with a white stomach. I do not doubt that there may be a few that are different colors out there but sugar glider come in many different colors and no two are exactly the same.