Matrix

I'm currently trying to set up my own matrix instance, and most of it is working, except for the federation. Due to technical reasons the only way to host anything is over Cloudflared. I know it's not perfect but it is what it is. So now here's my problem. I'm currently trying to get federation working, but I'm a bit confused about the documentation. Also, I'm using the apt version, so for some reason most of the Directories are also different... If anyone did this before and could help me with this, i would be really thankful.