When you case an Improve Attributes or Improve Reflexes spell normally, if you have more than one success and want to keep the extra successes you can, at the cost of extra drain (1 more drain for each extra success you decide to keep).
However with preparations you pay the drain well before you ever see the result of the spell being cast, so you don't know how many successes are available. I suppose that the logical thing is that when casting the preparation you decide how many extra successes you are willing to support, and pay the drain on them.
So for example, you create an Improve Logic preparation, which normally has a base drain of 3 and as a health spell has to have a command trigger (+2 drain), but you want to be able to get two successes when it goes off, so you increase the drain by one more to 6. When you finish making the preparation you are resisted by the drain (6) but hopefully end up with some successes, giving you potency = net successes. When you command the preparation to activate you roll (remaining) potency + your magic, vs a threshold of 5-essence, and hopefully get at least two net successes (and if the target has an essence of 6, this means only needing to roll one success).
This sound about right to everyone? Or do you see it differently?
(and yes the question is pretty abstract, because alchemy is so painful in 6e that I doubt I'll use it, but I was looking at converting a 5e character concept over and was trying to figure out how things would work).