@Tod. Yes, having ‘played’ with Encoder I see that I can import my AE project, select the composition to export etc.
You say that the H.264 exporter is much better in Adobe Media Encoder – what do you mean? Are you saying that I should use Encoder to create my .mp4 rather than rendering in AE? What about rendering .flv files? Finally, in Encoder I haven’t found how to export to .webm or .ogg – which format should I be selecting?