Books are the greatest gift.

I've started on getting the maps into the atlas. First out is Quenten's "Bowmans General Store":

Personally, I've just used them as visual aids and planning aids (but then again, that's what I use most of the maps for). Isometric isn't the best for battle maps, but at least in my world, battle maps are in the minority anyway, illustrations and planning tools are much more important, and for that, isometric gives a very nice easy to understand view of the place.

One I used recently was an outside view of a ruin

Some compass roses would be nice also on city/street maps, such as Arthenn and the docks. Looking at the bridge and the parent map, it is clear that north is to the right on the docks map, but this can't be seen from the map itself. Preferable, any map that doesn't ashere to the modern convention of north up should have a compass rose to indicate this (Personally, I like to see them on most map anyways).

Wouldn't mind seeing some scale bars as well, makes it easier to use the maps.

The pain with automatic replacing symbols in the same spots is that it is vulnerable to the scale and origin of the symbols you switch. Most of them are not designed to allow perfect replacement, so even doing it automated usually means things doesn't look quite right. In most cases, when a style have both living and dead trees, the dead trees aren't the exact same tree as the living one (but without leaves), but rather a new tree the artist drew.