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Please go to Province Defence for information on Province Defence.
Fort-less provinces draw from the independent local population for their Province Defense. The second Commander and extra troops (from the 20th level onward) are from the owning nation, however; this would be the more-professional garrison, whereas the local troops could be seen as the militia.
Forted provinces do not draw from the independents at all; instead, their standard Province Defense is the sort of troops that fort-less provinces would otherwise only get from the 20th level onward, while the 2nd commander and extra troops from the 20th level onward are typically higher-tier units. The 2nd commander for forted Province Defense is typically a Priest, or the nation's Mage-Priest.
Underwater Province Defense and on-land Province Defense are not the same, of course. Some nations (typically Underwater ones) have a separate Province Defense for coasts, too. If a gap is present for coasts, the on-land Province Defense is used instead; and if there is no on-land Province Defense, then the independent list is used, even if the province has a fort. Likewise, if a nation without an underwater Province Defense takes an underwater province, levels from the 20th onward will not be improved.
Some nations have cultural or historical bonds with certain independent types, giving them a decent discount on Province Defense levels; for example, the Bandar Log has kinship with the lands of the Atavi. Ironically, the capitals of nations do not get this.
The Province Defense is not immensely respected by your more professional armies, in case them being treated as a separate army under your flag wasn't a clear-enough tell. Their squads are roughly the same as the different rows in the Defense menu, and your stray troops simply left in the province are not integrated into them. Despite being a separate army, they HP-rout with your professional army, and technically can be the ones to cause an HP-rout; however, their HP is only 25% as relevant as that of your professional troops.
You can't script or reorganize your Province Defense, but it replenishes each turn for free. The only way to totally wipe a Province Defense level is by taking the province for yourself, or by killing the entire local population with Lost Land or other magic.
Ultimately, some nations have much better province defenses than others, especially for the cash investment required; and on the other hand, some nations are far better at trivializing Province Defense than others, whether through immensely powerful units or Commander-sniping shenanigans.