Not a stupid question at all — this is actually something a lot of people wonder about when they start using choice spreads.
Yes, typically you assign each side before you draw the cards. So you decide in advance something like: left column = option A, right column = option B. That way, you’re not trying to “fit” the cards afterward — you’re reading them in relation to a clear structure you already set.
Some readers also like to physically label the positions (even just in their notebook or in their mind) before shuffling, just to keep the intention steady while drawing.