This is how it was explain to me by a CM:
On the side of Tomorrowland, the bobsleds run on the inside of the mountain & it is supposed to be faster.
On the side of Fantasyland, the bobsleds run on the outside & it is supposed to be slower.
Everytime we have been at DL, they have had both sides open & they operate as different lines, right for Fantasyland side only, left for Tomorrowland side only.
The best experience is to ride both sides & choose your favorite. I personally love the Fantasyland side during the nightime.