You'll want to change uNumDepthGrids to 1 for creating local maps, otherwise some water cells will contain transparent water (due to the increased ugridstoload).
I do prefer the results of the in-game local map creation over CS creation, because it hides all the x-markers, map markers, activator boxes, collision boxes, sound markers etc. along with the water being included. It's also quicker at generating the local map than the CS, and is capable of mapping more cells in one go than the CS.
Do you know about the coe console command? Instead of coc, you can use coe to go to specific cells, e.g.
coe 22,13
This will save having to edit cell names before loading the game. This is my preferred teleport command, but you might be quite happy with coc of course.
I kept running into cells where the water color was non-existant, so I went back to the drawing board.
I've found that making changes to the ini is unecessary except to change the uGridsToLoad (and maybe the ipreloadsizelimit - I left it at 52428800).
For map generation, the only ini changes I have now are:
uGridDistantTreeRange=9
uGridDistantCount=9
uGridsToLoad=9
iPreloadSizeLimit=52428800
All that is needed to generate high quality local maps is to turn off Distant Land and all the water settings in the Video options.
With all veiwing distances set to 100% this is what I get using 7, 9, and 11 uGridsToLoad (in clear weather).
http://i429.photobucket.com/albums/qq11/aellis-photos/example.jpg
There is no noticeable differrence between 7 and 9 grids, but at 11, the shallow water begins to fade. At 15 (which is what I used), the water color is non-existant.
Changing the weather type changes the shade of blue.
Since there would be more work involved in touching up what I already did, I'm going to regenerate the lot and start from scratch.
This will delay my contribution of course, but I'd rather give something outstanding rather than "make do".
You probably missed my earlier post (quoted above) - you need to set uNumDepthGrids to 1, this will resolve the water in some cells becoming transparent. Or do you refer to some other water issue? What weather are you using now, Clear, 38eee? It would help TheNiceOne if our resulting local maps matched, so if you're switching to Clear, I will too.
EDIT
TheNiceOne, I've redone ULs Ancient Redwoods and Ancient Yews with clear weather, so the water is blue rather than grey. Also I've created local maps for Arrius Creek and the linking patch between Ancient Yews and Arrius Creek.
http://bettercities.free.fr//UniqueLandscapes/Maps/UL-AncientRedwoods-Clear.7z
http://bettercities.free.fr//UniqueLandscapes/Maps/UL-AncientYews-Clear.7z
http://bettercities.free.fr//UniqueLandscapes/Maps/UL-ArriusCreek.7z
http://bettercities.free.fr//UniqueLandscapes/Maps/UL-AY_AC_LinkPatch.7z
I only just noticed that you asked how I made trees appear and water shade as white when using the CS. I no longer intend to use the CS for local map generation, but if you're still interested then for the water, edit ConstructionSet.ini and change WaterShader to 1.
For the trees, they will only appear in the cells first loaded and not in any cells loaded later.
The cells first loaded are dependent on the ugridstoload setting in ConstructionSet.ini, centred around the bottom-left most cell of the grid you chose for local map generation.
If ugridstoload is set to 11 (any higher and there's a good chance the CS will crash) and you want to generate local maps for cells 0,20 to 10,10 (the entire Imperial City plus Weye), then the starting cell will be bottom-left, 0,10, and the ugridstoload of 11 means that the first cells loaded around the starting cell will be -5,15 to 5,5 (most of which will be ignored as they're not within the grid you're generating the local map for)
So cells 0,15 to 5,10 will include trees. All the other cells will not include trees as they are outside the ugridstoload radius of the starting cell, so you would want to reduce the size of the area you're generating the local map for and run it multiple times until you have covered the entire area.
First 0,15 to 5,10
Then 0,20 to 5,16
Then 6,15 to 10,10
Then 6,20 to 10,16
And that gets trees in every single cell!