Is this translation correct? I don't know how you get 'of your knees' from the Czech. I would translate it as Which knee hurts/is hurting you.
Both are accepted.
Why is ''Which of your knees aches?'' not correct?
Alternatives with forms of "ache" have been added.
Which knees of your is hurting? - I know it's uncommon, but I feel like it's right though.
I am native AmE. You might hear "Which knee of yours hurts/is hurting?" -- but (1) that's slightly different from the suggestion in your comment; and (2) it may or may not be accepted because it's also (at least to to me) a little unusual.