In the recent Mighty Avengers (during Dark Reign or Siege) They established the differences between Pym, Stark, Richards, and Banner
Reed is the explorer
Stark is the engineer
Banner (?) the tormented scientist or something (I don't know)
and Pym was named as the Scientist Supreme
Not because he is smarter than the others, but because he works to make the impossible possible, Richards explores and discovers things (although he always invented things to save the day in the past), Stark builds inventions,
Pym invents things, explores things, and uses all sort of science (genetics, chemistry, engineering, so on) to make impossible things happen.
So I guess in the movie Stark is the inventor, while Pym is the all around scientist that dabbles in everything from engineering, chemistry, genetics, and so on.
In the movie he shouldn't be smarter than Stark though, he should be somewhat over looked, with being on a team with Stark who is a super genius, hansom, rich, and loved by all. He feels inferior to him. But that shouldn't be presented right up front.
It could be slightly hinted at a little. Then expand on it in the sequals, showing that Pym feels inferior to everyone on the team.