I just tie it in with the birth story. My dd knows that when it was time for her to come out of my tummy, she got stuck and the doctors had to operate to help her get out. And she is a special baby, cos the doctors helped to make her as well, cos we wanted to have a baby very much but daddy couldn't help mummy, so a special man at the hospital helped instead. We are very glad that they helped us to make you!
Dd is 4 so yes this goes completely over her head, although she is starting to tell parts of the birth story back to us and apparently she shouted 'help! get me out, doctors!' while in the womb
Just keep saying it, answering any questions they ask you, keep it as simple as you can.
We are a straight couple, and my dd recently expressed shock when I said yes woman and men can get married and also a woman can marry a woman, and a man can marry a man. I wish now that I had discussed this kind of stuff a little bit earlier, it doesn't take much for these kind of subliminal messages to go under the radar.
I don't think you can do it too earlier, if they don't get it they will just dismiss it and then ask again a few weeks later - but I think that you can do it too late.