There is a separate download console right now, but the design is such that there will be only one eventually. Try setting the AccuVote version to 2.0 and you will get another tab in the download v2 dialog to download to version 2 AccuVote units (we should also hide the v1 menu, but don't yet).
Same thing for upload. The idea is to have results from regions, AV, and AVTS all come into the same dialog. Obviously we will rename the "receive regional results" menu when we do this.