I have the game and all its expansions, but I like the idea of having the GOTY version where the whole game is in one DRM Free installer, (I don't use Galaxy)

Without the GOTY version I have to install the base game, than install the patch, than install the Expansion DLC, than install the patch for the Expansions.

It was mentioned a while back that GOG was to approach CDPR to offer free upgrades. But that would also mean CDPR would have to do this for all stores, not just GOG. We're still waiting so I'm unsure if this will move forward or not. In the mean time, GOG has suggested using Galaxy to take care of the install for you. I'd post reference links but I'm too lazy. sorry

I think in time it will happen. I just don't know when. The problem is probably with the XBOX and PS versions because there it's probably more complicated/expensive to do the same.

Just a couple of days back I saw one of the blues tease exactly that for the foreseeable future...

And here you go

https://www.gog.com/forum/general/upgrade_to_the_witcher_3_wild_hunt_game_of_the_year_edition_11c50/page1

So how do I make it work?

I don't see the option to upgrade it to GOTY?

Note: Currently, there is no time limit to the free upgrade and it's available to all users. You will be notified by email when the GOTY Edition gets added to your account, but for those already eligible this process may take up to a couple of days so please be patient.

K thanks.

You have to wait as upgrade will happen automatically.
You will get mail when it will be added to your library.