For basic business travel on AA, it tends not to matter. Other airlines routinely penalize travelers for buying the cheaper tickets. On AA, you have to work pretty hard to find a domestic ticket which will penalize you by not awarding miles.

The basics are
F=First
J=Business
Y=Full fare (expensive) economy

See here for some more info
http://www.aa.com/content/AAdvantage...irements.jhtml