"Although he is sick, he did not take a day off."
Always pair duolingo with some supplementary, explanatory material! You are not going to learn chinese, or any language, with duo alone.
In this case, the subject can go before or after 虽然. As far as 了，it can go at the end of either phrase, depending on the meaning. If both phrases are in the past tense, you only need to put 了at the end of the 但是 phrase.