In general, you ought to be able to just read a poem naturally and have the pattern of stressed an unstressed syllables emerge. It’s a job for the poet to arrange words in such a way that the rhythm they want is present in the poem, which is why fixed form poems often employ an expanded vocabulary and unconventional word order.
But while the form is supposed to be a framework for the poet—a tool to narrow down an otherwise infinite field of possibilities—it is sometimes leaned on too heavily, shifting the burden to the reader. In such cases, all you can do is recognize the form and read accordingly.
If you have a particular poem you’d like us to look at, please feel free to share it. I, for one, would be happy to go over it with you.