The "pick/choose your poison" idiom conveys that someone has to make a choice between two unpleasant options:
Hiring a carpenter is expensive and doing it yourself is slow. Pick/Choose your poison.
Removing your wisdom teeth means a painful visit to the dentist, but if you keep them you might have gum problems. Pick your poison.
Commuting using public transport is unpleasant and uncomfortable, but buying and maintaining a car is expensive. Pick your poison.
It seems that the origin is simply that since the mid-19th century "poison" has been slang for alcoholic drink. This may refer to the Latin root "toxicum" (meaning "poison") of the word "intoxicate", or it may just be a reference to the bad effects of excessive drinking. Thus the phrases "what's your poison?" "Pick your poison" and "choose your poison" arose naturally.
What I'm actually trying to translate is
Pick your poison and I'll pick mine.
Which of course conveys "you make the choice you want and deal with the unpleasant consequences of it and I'll make my own choice and deal with the consequences of it."
I was hoping that there would be an idiom for it in Spanish. Closest I could think of as of now would be "Estar entre la espada y la pared", but in Spanish you don't tell people "Decide si quieres la espada o la pared". You just use the idiom to convey that they are in a difficult place of between two unpleasant options.