Hi Mike,
You can create multiple routes, and access them via the My Routes list on the Favorites screen. Tap the Star icon on the Route Info Panel to add your route to the My Routes lists for later use. To remove the current route from the map view, tap the X button in the top right of the Route Info Panel, and you may then start another route.
To remove a point from your route, tap the X button next to the item’s name. If you do not see the list of route points, then double tap on the Route Info Panel first to show the route’s destinations list.
You can also just press and drag to reposition a misplaced route point. Note that the current version of PocketEarth is limited to 10 route points per route.
We are doing major work on the routing system for our next update v1.3, please see this forum post for more information.
You may also be interested to know that our routing service provider, Cloudmade, does support routing over ferries, provided that the correct routing annotations are available in the OpenStreetMap project. The great thing about the OSM project is that anyone can make corrections and additions to the maps through their website.