Try Bright as the Sun/Bold as the Moon by Affectingly. Derek finally works up the courage to ask for something, and Stiles is more than willing to help. (http://archiveofourown.org/works/520450)

I don't know if the Alexandrian Solution by Bexless counts as negotiation, exactly? Stiles and Derek are both surprised to discover Derek has a knot. They process this first verbally before continuing to have sex. (http://archiveofourown.org/works/489654)