The S6 Map editor is a very complex program to get to grips with and it has a number of glitches the secret is to SAVE your work REGULARLY as it can often crash for no reason or some glitches cannot be undone.
There are a few turorials on line I am sure if you search around you will find them.
I made some cracking maps back in the days. yes every detail has to be added and checked. I seem to remember that it was usual to make a single sector of a map and then duplicate it to make the complete playing area.
It is a long process and in order to make the maps playable they need to have a point or a focus to work properly.
Personnally I think settlers 6 was the best of the series but everyone has their own opinion the map editor program kept me busy for many hours between games creating levels from scratch that contained every detail from flowers to animals and carts.
Water was always a bit fiddley to get right and if you are not careful you could flood large tracts of land by mistake.
It is a good editior just need to find help online on how to use it. I no longer have my links but remember that pretty much everything you needed to know was on there.
Since the abandonment of settlers 7 I haven`t been playing my friends and I have gone back to Unreal Tournament as there is always something new to do on there.
i found the map editor in Computer/ Local Disk / Program Files / Ubisoft / The Settlers - Rise of an Empire / base / bin / S6MapEditor. you can double click S6MapEditor and start the editor, or right click and send to desktop ( create shortcut ) and run it from there. This is on a 32 bit windows 7.