Answer provided 14 Nov 2014:
Q: On the heightmap of that terrain I can see a lot of blue areas which means that these areas are below sea level. This is probably right because we have some regions that are below sea level.
When I finalize the terrain and pack it I see that all those areas are covered with water.
Is there any way how to define the coast line so these areas are not covered with water in the final terrain?
A: Currently, we manually adjust (using photoshop heightmap editing) the maps that require us to deal with areas below sea level that are not actually under water. There is no ability to do this at this time with the Terrain tools we offer. This is something we could help prepare for your organization through our program called Professional Services.