Not a stupid question at all. Lots of people wonder this when they start using choice spreads.
Yes. Usually you assign each side before you draw. Decide beforehand, for example left column = option A and right column = option B, so you aren't trying to make the cards fit after the fact - you read them against a structure you set up first.
I often physically label the positions (even if it's just a quick note in my journal or in my head) before shuffling, just to keep the intention steady while drawing.
