The difference: personal preference. If you are talking about race stock skis, they all will be well competent for amateur racing. Period.
If you are talking about retail "race" skis, the difference still is personal preference, assuming you are skilled enough to know how to drive a race ski. To me, Fischers offer more stability, more torsional and longitudinal stiffness, and edgehold that scars the mountain. Atomics feel lighter and snappier, have more "pop" (some like that in a race ski; some don't), and are a little more forgiving. I think the Atomics are probably more versatile for all-mountain skiing.
Both are lightning-quick edge to edge, if you have the skills & boots to drive 'em, that is.
At FIS minimum length, I'd choose Fischer for a true GS course and Atomic for Nastar/beer league (actually, I'd ski a Fischer SL in a NASTAR course and regularly do). But that's more of a reflection of my skiing style and taste in skis.
There is also a conventional wisdom that states that Rossi and Elan are better choices for lighter skiers. But when you go watch some junior races and see what skis the J1s and J2s are on, it is usually more a reflection of what brands have active reps at which home mountains.