Configuration Manager for Jira 4.1 – welcome on board!
Since CMJ 4.1 you can include Dashboards in snapshots (either project or system). The interface is very similar to the ones for filters and agile boards. For project snapshots this can be done on the fourth page of the snapshot creation wizard.
On the preview page of the wizard you can review the snapshot details and the selected dashboards and exclude some of them.
You can also include all dashboards in system snapshots.