When I set up mine, I...
release cable,
Shifted all the way down up front,
Set lower limit screw, chain in small(front) big(rear)
reattach cable,
Shifted up (to former middle ring, now big ring)
Set upper limit stop screw,
tweak as needed,

This gave me a trim option in both rings... tho I never use the trim on the big ring, and rarely use the trim on the small (no need if adjusted correctly)

I think that's about it.

edit* this is with 105 9spd, no derailleur change. I (today) changed to a short cage rear derailleur, and it seems to have helped with rub when crosschaining (maybe I just have it set better... I'm to ocd to leave the long cage). I have a double 105 front derailleur on the way, and it shoud help fine tune the shifting up front, and make it smoothier and faster.