Roadie,
If you want to adress the symptom (functional leg length)... set seat height for longer leg and put spacers under the cleats to address the short leg. If you want to address the problem get a bike fit from some one who knows howto see the big picture... by setting the bike up to your physical abilities, helps you with posterior chain leaknesses, and pelvic malalignment.
Good Luck,
V.S.