You'll roll your dice against twice the force of the preparation you're creating. So in the case of F6, you'd roll 18 vs 12 dice, with net hits being the Potency.
When triggered, the preparation rolls Potency + Force (with a limit of Force) to determine the spell's effect.
So a P2 F6 preparation rolls 8 dice, and a P6 F2 preparation also rolls 8 dice, but their limits are different so obviously the higher force is worth it if you can get away with it.
OTOH while high Potency doesn't help you with the limit, it does help you with shelf life and duration. And it's the easier value to pump up... you mathematically get a slightly better than 1:1 return by lowering Force! Also, one of the key advantages of preparing the spells ahead of time is you can blow resources like edge during downtime and then potentially recoup them before the next mission.