Hey, I recently accomplished this.
You have to host the .well-known via a reverse proxy and then point CT to the reverse proxy, like @manwichmakesameal@lemmy.world said. Personally, followed this guide and here they talk about how to serve the .well-known. You don’t have to follow it exactly, if you already have a working Synapse server.
I hope I could help you and if you have any more questions feel free to ask.
Edit: formatting
Just got it and I must say, well done! It’s not as feature rich as some of the other apps but it looks nice and works well. I think with some more updates you’ll be at a point where this is my favorite Lemmy app. Great work!