It's a hole, which rests in some spot just like a normal hole. It doesn't destroy whatever it is resting on, only what is brought into contact with the "surface" of the hole.
I think the answer it's either nothing (see above) or the other standard answer when dealing with bags of holding acting up which is....massive explosion
I think that if you put the sphere into the bag without touching the bag, it will be resting safely in the extra-dimensional space. If it touches the bag you lose your bag and the sphere remains in the prime material plane.
once you figure out how to get the sphere into the bag, come back and ask again. a bag of holding is 2' wide. so is the sphere of annihilation. not much room fo error i'd say.