I downloaded my game to 1.6.659.08 and SKSE 2.2.3 yesterday. The game works OK, but it won't point to my mods at all and I can't find out why.
My staging folder in Vortex looks like this:

[USERDATA][game}\mods No mods show up in this folder BTW
C:\users\kdrat_fu1mhv\AppData\Roaming\Vortex\skyrimse\mods The mods are here

Do I need to change the first staging folder line in Vortex and name it for
the second one for it to work? I am lost and don't want to mess it up.

Thanks for the help!

In Vortex, I go to 'Settings' in the left-hand menu. Choose 'Mods' from the tabs in the main window, and set a folder for the staging folder here.

It doesn't need to be a particular folder (Mine's in D:\Games\GOG Game Files\Skyrim Mods Staging Folder)
To install mods, I just drag the zips into the space at the bottom of the mods page (click 'mods' in that left-hand menu column) where it says 'drop files'.

Vortex then copies the relevant data to the staging folder and then deploys it to the game directory.

Hope that helps - if not, clarify what you're doing differently and I'll try to help.