Just install Skyrim AE and click "Add to Vortex".
Everything should work right away. A very simple collection for users struggling to figure out how to get this to work.
Launch regularly first then open (C:\Program Files (x86)\Steam\steamapps\common\Skyrim Special Edition\Data\SkyrimTogetherReborn) and launch the "SkyrimTogether" application. Then launch normally. It should all work. If you want to host a server, in the same folder is an application called "SkyrimTogetherServer".