If you are putting together a FOMOD installer, I don't know how to set that up, I just know that there is a setting that should be different for MO2 and Vortex. Something about including the Data folder.
For other mods. Just assume that your mod will be extracted into the Starfield directory. That means that any files you intend to install in the root directory should be in the root directory of the mod. MO2 and Vortex will grab an archive that just has an esm file and put it in the correct folder. Vortex won't put textures and meshes in the correct folder unless you include the Data folder correctly. For example .\Data\Textures\Clothes\...
I hope that helps! Happy modding.
