working on a map from an online rpg: The miracle, map 1 - Kingdom of the Westlands

[EruSilme]

I have started the work, as i said, with the magic wand tool: there are probably a couple of shades of blue, so i changed the tolerance to 6 and added (pressing shift) the majority of water areas i saw on the map (rivers, lakes), then i saved the selection in a new channel for futher use.
As maybe you can see if you look closer, some of the man-made (sometimes elf made ) structures stretch out on the water, and they are often large enough.

Therefore, wishing to have a selection that included only the "coast" i had to switch to "Quick Mask" and manually delete these areas, such as port facilities on the Isola dei pescatori, the bridge of Hammerheim and the piers of Rotiniel (the elven city that is seen in the upper left corner).

Even now, I see a problem I may face in the nearest future, and on which I would like to admit some advice: how to manage the city?

It is clear that, by the very nature of the game map, the cities are very "large " compared to the map itself.
On the other hand I can not even put a tiny marker in the middle of the island of Hammerheim, and say "there is the capital", when virtually the entire island is covered in buildings.

The solution I had in mind was to depict the houses themselves, essentially, using the original map as a track : so to speak , something like this http://historic-cities.huji.ac.il/br...rg_III_2_b.jpg

The buildings are not many, although some might create a little bit of problems ...
It ' a setting that I've never tried, but I would like being able to adopt for further use! Simply i am not an artist

The alternative could be to adopt a top-down view of the city, but at that point I guess I should also adapt the rest of the elements ( mountains and forests ) to this point of view, giving up the isometric one.

maybe i am missing some alternative?