Here's a map I made using the Chitty City tool I posted the other day.
I drew the chits randomly, but placed them deliberately so that they made some sense in relation to one another. I'm looking at this map now as a PC would, wondering why there's a colossal unfinished statue on the prison island. Are the prisoners forced to labor on a huge statue of the city ruler, or perhaps of a god that will come to life when the statue is complete? Maybe the colossus IS the prison, like some huge Wicker Man full of criminals. And why is the city center an abandoned killing field? Is it accursed? Plagued by undead? Whose tower is that? Zenopus? Maybe it's Porttown from the Holmes sample dungeon!
Once I'd placed all the chits I wanted, I took a Sharpie marker and drew a shoreline and a few rudimentary geographical features -- no artistic ability needed for this sort of exercise.
I could add as much detail as I wanted from this point: bridges, plazas, city walls, entrances to the inevitable underworld beneath the city. And plenty of space to make notes directly on the map in each section. If you try one on your own, make sure you send me a link!