Often this is caused by not launching Skyrim Special Edition via Steam at least once before starting the modding process. The steps to solve this issue vary depending on which mod manager you used:
Vortex, by default, uses the same location for configuration/INI files as unmodded Skyrim. You simply need to close Vortex, open Skyrim Special Edition Launcher via Steam, click Options, set your graphical properties, and then exit the Launcher. When you re-open SkyrimTogether via Vortex your problem should be solved.
MO2, on the other hand, defaults to using custom INI location per profile. In the top-left of the MO2 window is a drop-down list of launch targets for Skyrim. One of the options should be Skyrim Special Edition Launcher: select this option and click Run. Once the Launcher is open, click Options, set your graphical properties, and then exit the Launcher. Chagne your launch target back to SkyrimTogether and click Run.