There are many ways to do this. You can create your motion menu in AE and have your buttons come up and then ride that out for a set time…say a minute or two. Then in Encore, set the Loop point to the time at which the buttons in the animation have come up completely. The loop point is the point at which the button overlays will appear. At the end of the two minutes it will loop back to that point again.
The other common method is to create your animation, have your buttons come up…Export a still frame from AE of the menu with the buttons all the way up. Import the animation in as a timeline and import the still frame PSD as a menu. Set the animation as a first play and have the end action for the timeline be the still menu. When the disc is inserted, the animation will run, the buttons will come up and then it will drop you to a still of the menu with your buttons and overlays.
There are other methods I’m sure…these are just a couple of ways to do it.
Erik