Place river tiles from the headwaters to the estuary linearly; it's the only way to get them to lay out correctly. As far as things that can't be deleted, it happens; you can save the map, restart FE, and reload it and things should be OK for awhile. You can also delete and place things like starting locations from the mapname.xml file if you can't get it to work through the app.

Yes it is buggy as hell but you can make the maps you want with a little ingenuity, at least until, if ever, it is fixed (It was exactly the same in WOM so don't expect a fix soon.

Ok what is the mapname.xml file? A yes the editor is boggy as hell, and the mixture of creatures and quest leveled to your in game avatars are very disproportioned.

I have been trying to build an FE map as well. I was able to change starting locations the same as WOM, however they all disappeared along with all my quests! Even after restarting the game and reloading the map, still gone! Then a week later i decided to try again, loaded that same map and to my surprise, all the quests and starting locations were back!!.... figured they must just have been on holiday or something???