I've used green to show areas that have a loyalty to the Church, are settled, and relatively safe. Yellow is for specific adventure sites and / or encounters that aren't always going to overlap with the Church's laws, goals, etc. Red, is mostly for monster-controlled territory or ranges, specifically dangerous sites, and anti-human or anti-church things.
The zones of influence suggest a lot to me at a glance: who might know what about things in the area; who you might bump into when you're out and about; where the secret / valuable stuff is; what kind of re-skinned monsters ought to go where. Zak had a post about zones a short time back too. For me, the coloring works as a way to get some better info at a glance. (In reality, I don't know what the "X" with superscript next to them are intended to mean...so I did this instead.)
Its not quite finished, but I've certainly gotten a better idea of the map and the map key overall than I had before. Welsh Piper's thoughts about world building, turf, and letting random tables guide the wilderness exploration experience have produced some interesting results. I've not added all the overlapping territories yet, as I wanted to focus on the areas around Blackmarsh Castle to get a better idea what starting characters near there might face. If you're checking my work, you'll note that I didn't really fill in some of the full "ranges" suggested by the size of some of the encounter monsters...thats because I was in a hurry and more interested in settlements and the like.
With any luck, I'll be able to figure out a way to tag a PDF version of this map with "stickies" or annotations that I can simply click on during a session to get a bit of detail of each 5 mile hex. Then, maybe add some custom encounter tables for zones, and BAM...its all over but the treasure rolls...right?