So, a bit of background for the setting:
Shadowrun canon involves a world in which everything magical disappears for thousands of years at a time, only to return from the depths of prehistory in a sudden unexpected reveal. This setting has magic become greatly restricted in extent, but not disappear completely, during those low-magic eras. During the Fifth Age, specifically, the small surviving magical component of the world chose to actively hide from everyone else, altering the dynamic of the past in a variety of ways. That is a very big change in the setting, and as a result, entire stretches of Shadowrun historical canon will be significantly changed.
For instance, in the back-history of the collapse of the USA and the formation of the NAN, Daniel 'Howling Coyote' Coleman canonically managed to make great inroads because he was one of the first magic users to reappear, and he used that novelty to engage in his unique form of aggressive homebrew vulcanism essentially unopposed. In this setting there is already a magical government in place with their own, much more experienced, magical combat personnel. The Confederacy is unlikely to be particularly tolerant of some young dumbass setting off volcanoes in their territory, nor are they particularly sympathetic toward their now quite distant non-magical cousins. The resulting political landscape of the Sixth World's North America is thus going to be quite different, or at least formed by different forces, than the one in Shadowrun canon.
As for the current structure of magical North America, the Shadowrun Native American Nations didn't form until 2018 when the Treaty of Denver recognized their sovereignty and ceded the western half of the US and Canada in exchange for an end to Daniel Howling Coyote's string of volcanic mass-murders. At the moment in-story, Howling Coyote is nearing his second birthday on an Indian Reservation somewhere in the US, so if we were dealing solely with the Shadowrun nations, everything would still be firmly under the control of the normal U.S. and Canadian governments at this point in history.
By contrast, the Confederacy in this setting has existed to one extent or another for over fifteen hundred years (I'm using the legendary accounts of the formation of the Haudenosaunee nations, rather than the currently accepted historical consensus that places the founding much later). It began as the original Haudenosaunee Confederation (a.k.a the Iroquois Nation), which formed around through the efforts of Hiawatha, Jigonhsasee, and the Great Peacemaker. I have them separating from their non-magical counterparts sometime in the eleventh century AD and going their own way, much like most every other wizarding society in the world (odd how widespread that tendency was, one might call it suspicious). The other native tribes went through their own wizarding secrecy movements as well, and while the non-magical remnants did their own thing, remaining separate until the eventual European colonization, the magical side of things banded together over time into the Confederacy, due in large part to the constant threat from their hyper-aggressive neighbors to the south.
As a result, the wizarding side of North America consists of two macroscale political entities: Aztlan (the Aztecs) which is a notoriously violent theocracy whose primary form of worship consists of sacrificing captured slaves and ritual cannibalism; and the Confederacy; which is a loose voluntary federation of everyone else. Nonmagical political divisions are entirely irrelevant in this context. European colonization never included many wizards, so there is no magical US, magical Canada, or any other magical equivalent of the modern nations of the western hemisphere. Aztlan coincidentally occupies close to the same space as nonmagical Mexico, but the two entities are not actually linked.
The closest ties between the two worlds in the western hemisphere are actually the drug cartels, which bridge the magical-nonmagical divide. They were created to push the Awakened drug, cocaine, which, in addition to generating a great deal of non-magical currency, also serves as part of a distributed blood magic harvesting scheme to draw magical energy from the suffering resulting from the drug's use. The power collected is a large part of why the Aztec blood mages are so feared. The South American cartels are run by the Inca (who originally developed the magical coca plant and its use), and the Mexican ones are tied to the Aztecs (who stole it from the Inca).
As a general note for the setting, wizarding national borders are generally independent of the non-magical nations occupying the same territory with three notable exceptions. The first is Britain, which is nominally tied to the non-magical royalty by lingering oaths which were forced upon them by Merlin during the time of Camelot. Though it should also be noted that between the secrecy policies and the historical changes in the royal bloodline, those oaths are very loose at present time. The second, Japan, is under much more binding sovereignty magics tying them to the Chrysanthemum Throne; however, a bit of political scheming and some targeted regicide has essentially rendered the binding almost entirely irrelevant on a practical level by making it impossible for the current Emperor to issue official commands to his magical subjects. The last is the Magical Romanian Empire, the emperor of which was originally the entirely non-magical Voivode of Wallachia before he became magical due to an accident. While the Empire has greatly expanded in the five and a half centuries of its existence, its European border remains unchanged.
