You can create a timecode counter in Premiere Pro and/or After Effects. You could also use those apps to create a progress bar.
If you have the Production Suite, then you can use Dynamic Link to set up a live link to an AE composition, which would allow you to easily make changes in AE and have them show up immediately in Encore, without having to render from AE first.
Use exported footage from PPro or the linked comp from AE as the video track for your audio timelines.
-Jeff
The Focal Easy Guide to Adobe Encore DVD 2.0