It's not in App Store updates and when I click on the beta 2 in my developer account it tells me the code has already been used.
where is el capitan beta 2?
There won't be an el capitan beta configuration utility till after public release.
The developer previews that come before public release should already be configured to receive the subsequent developer previews and golden master.
You're quite right, in 10.11 my App Store PrefPane doesn't have it either - At the time of writing, another poster indicated that setting the update catalog correctly should make it re-appear. I took it on board without checking it myself - I'll remove reference to it.