It would usually be CLEAR up and CLEAN up. However, it could depend on the context if you're stressing a word for emphasis. For example: We were the only food vendors at the conference, so we really CLEANED UP! Did you clean UP before dinner? It looks like it will rain. I hope the sky CLEARS UP before the picnic.

Phrasal verbs and the stress patterns of phrasal verbs are a bit complicated. Here is an article that might help you. At the top of the page click on the link: Getting the stress right. http://www.macmillandictionaries.com/MED-Magazine/October2005/34-Phrasal-Verbs-Pron.htm

I meant whether the stress in, for example, "clean up" is CLEAN up or clean UP

Your question is somewhat unclear. But generally speaking, if the preposition part of the phrasal verb is at the end of the sentence, it is stressed but in the middle of the sentence, it is unstresed. You need to clean up. -- The stressed words are 'need,' 'clean' and 'up.' The words 'clean' and 'up' get the same stress. But You need to clean up the mess. The stressed words are 'need', 'clean' and 'mess."