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If you are asking how SKSE64 works with mod manager, then you can run it through the mod manger (Vortex or Mod Organizer 2) like any other application. It then reads what mods you have in virtual Data folder (MO2) or as symlinks/hardlinks in your Vortex profile.
Edit: I am unsure if I understood your question correctly.
Mods that use SKSE will check it's version on start and run it's features without further interaction or tweaking, if game is launched through SKSE launcher.
Mod Configuration Menu (MCM - comes with SkyUI) allows tweaking options to mods relying on SKSE, if mod author has added configuration options and MCM support for their mod. Not all mods require any configurations, so not every mod has MCM either.
https://steamcommunity.com/app/489830/discussions/0/340412122413706606/
and here
https://steamcommunity.com/app/489830/discussions/0/3050607936308054365/
and i have skse64 perfectly integrated into vortex. everyone told me to read the guides and i did, now my skyrim is working like charm. listen to the advice of the elders here, they are far wiser than i.