There is usually no difference in stress between the two syllables. Sometimes the stress is on the 'up, especially in compound forms such as "the police set him 'up." And if we are talking about a planned ambush we refer to it as a 'setup. But ordinarily when we set up a meeting or something like that the two syllables are equal in stress.
If you have a question about the English language and would like to ask one of our many English teachers and language experts, please click the button below to let us know: