You need to supply your own id1 directory and then edit the dockerfile to tell docker where your id1 directory is.
Just change this line in the dockerfile:
ENV ID1 id1
to:
ENV ID1 <wherever you've put your id1 directory>
Now build the image:
docker build -t quakeit .
And now run and create a container
docker run -d -p 27510:27510/udp quakeit
And that should all work fine :)
If you want to change the server setup then edit ffa/server.cfg and rebuild the image.