Do I have to start BG3 through desktop mode for mods to work?

I got BG3 Mod Manager installed last night, and I got a few mods installed. When I launched through desktop mode mods were there. But when I restarted the deck into Deck mode there were no mods.

Do I always need to start in desktop mode for them to work? Mostly I am looking for a mod that adds a toggle to the item tags rather than having to hold R3 to see tags.

I am not using the built in mod manager, it did not have the mod I wanted listed, highlight everything.