In the latest update of Ensembl, the developers added the ability to save configurations. This allows you to set your track views and analysis to a specific configuration and load that configuration at a later time. The blog post linked previously (or here) explains the steps to creating your own configurations you can save and return to. In the future they will be adding the ability to share your configurations with colleagues and other researchers.
As far as I know, NCBI’s Map Viewer does not have the same functionality (please correct me if I’m wrong).