From this policy statement we have the following quote:
Technical Reports, Dissertations, and Lectures: Internal
reports and memos distributed within an institution, lecture
notes, tutorials, seminars, and academic theses or dissertations
are not considered prepublication even if available online
and according to MIT's resources page (see subsection on IEEE):
Submission of new article by author that first appeared as part of author’s thesis
Theses not specifically addressed, but permitted subject to editorial discretion. Individual journals may have their own policies
From these two quotes, it seems that if the publication is allowed at all, then you won't have any problem with having put it online previously because IEEE doesn't consider that prepublishing. However, individual journals may not accept theses for publication.
The answer to "how would IEEE determine that I am not plagiarizing" specifically is simply "both have your name on them."