Transitions between areas rarely represent areas being physically next to each other. Rarely they do, but usually they represent some distance of travel between the areas. To run from the north of mistone to the south would really be like... 12,000 areas if every square meter was depicted, but.. doing that would be impractical, pretty much impossible with NWN and.. rather unenjoyable I'd think heh.
Flowchart style maps work well for this (not sure if this is what you're doing.) Then just draw the line coming out the south of fort llast and coming in the eastern side of Zainge river (or whichever side it is, I think eastern.) Your character really just walked X miles, but you don't have to go through it all (not to mention having all those areas would choke the server to death with the way NWN handles things.)
-TV