I am myself busy with a city map. And true words, it is turning out to be one complex map. So, I know how you feel.

What I can offer is questions you can ask yourself:
1. Why did the FIRST people to come to this area chose this place to build something?
2. What did those people build? (A fort, a place to fish, a place to launch their boats. ect.) (Remember, people tend to extend their structures when they settle in. So, where that thing started can have more elaborate structures.

Now, as a city centre develop, a market is build where maybe roads come together, or is the most accessible and those markets have a bit of space for people to sell their wares. There can even be rich merchants that build grander buildings close to the markets they run.

There should be points throughout the city where people go get their FRESH water. Fountains, wells, a river.

As a city get more complicated, there needs to be those who keep the order. Guard towers at key points. Or a barracks or something of the like.
Then you can start thinking of a ruler of the city thinking about having a grander building, so they build it away from a poorer district, somewhere with a desirable trait, like the view or access to something important.


See where I am going, I am building the city from what started it and expanding it depending on what kind of people keep settling there.

For the city I am busy with, the river caused it to be a place where the main road went through and so it became a more important point and this caused things like a need for guard towers and people wanting to live closer to the point.

So keep asking yourself questions, what would certain type of settlers do when they came to the city. The rich might buy up a district and corner it off with a wall, or not.
I hope that helps focus it a bit.