If on the otherhand, this was built as a fortified town from the start, then a question is was it originally build this large or have the fortifications been expanded beyond the original borders. If the later case, then the same type of thought process would be needed except the main buildings would be clustered around a central location and new buildings which are not required by a town would sprout up around that as the new walls built.
Of course, this all assumes that this is not a planned settlement where most of the people came in around the same time.
My art skills leave a lot to be desired, but am fairly good at city layout, so I think about these types of things (probably all those teenage years spent playing SimCity.) When I design a city I think about how and why each building is where it is. Likewise, when creating an underground lair/dungeon, I think about each creature I want to put in and design the whole thing to make sense. I had a DM one time that had a 100+ room (3 levels if I recall correctly) dungeon with a Beholder, Drow, an Ogre Mage, undead, and a Mind Flayer. It drove me crazy because those creatures would never be able to live in harmony in that small an area (well except the undead, who would just try to kill anyone that was not their controller). That campaign gave me a lot to think about in terms of what should and what should not be where both in town and dungeon design.
If on the other