Steam seems to think my Skyrim is not installed and tries to install whenever i use the launcher. I can play using SKSE but i need the launcher to change the quality settings. Is there a way to fix it because if i reinstall i'm afraid i'll lose my mods?

well you won't lose your mods as they should be in a separate folder. But since you moved Skyrim from the Steam folder and into the SKSE folder that is why Steam is trying to reinstall the game. I don't use SKSE but it sounds like you may need to put Skyrim back in the Steam folder to fix what you need to and then put it back in the SKSE program afterwards.

Thanks i'm new to pc so i wasn't sure about losing the mods. I was trying to lower the quality because i have a lot of mods but it might be better to reinstall anyway because i have deleted some that had scripts.

well always uninstall the mod before deleting it.

SKSE is a good thing to use. but the Nexus Mod Manager is a great way to install and uninstall mods if your not sure what your doing.