F4SE loader can't open Fallout 4 once I open game through steam for the first time

New to modding, I've been following the steps across several videos but keep running into this problem. I installed F4SE into my Fallout 4 folder, ran the F4SE loader and tested it by typing "getf4seversion" in the console commands and it displayed the version, all good so far. but once i open Fallout 4 through steam to apply the video settings (mainly to make it fullscreen), i can no longer open the game again through the loader. i have to go to "my games" and delete the Fallout 4 folder, this is the only way to get the F4SE loader to open the game again. anyone know a fix? i've been looking for hours on google.