First of all, what you're describing are not really metaphors.
A simile is where you say, "He walked into the room, looking like a giant fish, with a gaping mouth and bulging eyes."
A metaphor would be where you describe him as if he really was a fish: "He walked into the room, a giant fish with gaping mouth and bulging eyes."
You appear to be talking about symbolism, which is something else entirely.
This is when an object, location, event - whatever - represents something else entirely. For example, a character could break their glasses, and this would represent the fact that they are blinded to the truth. In other words, the object symbolises some deeper meaning or concept related to the story.
Now, as a rule of thumb, anything that you (the author) finds confusing, your readers will definitely find confusing. Therefore, keep things simple.
My instinct suggests that you should avoid getting bogged down thinking in terms of symbolism for now, and concentrate on writing your story: flesh out the places, the characters, their relationships etc. Symbolism generally arises naturally from the novel itself, or can be added/elaborated during the revision stage, rather than being forced in the beginning.
Edit: To elaborate further, based on your comment below. I understand you want to use the city as a symbol of their relationship, but the symbol will likely arise because of how the character(s) relate to the city based on their relationship. To make symbols work, the symbols need to mean something to the characters themselves, not just the reader. So what I meant by the symbols arising naturally from the story is because, if you've told the story of the relationship between characters, the symbols you want to express should become clear to the reader.
To make a random example based on a man and a woman: a man is walking down the street when he passes by a restaurant that has been gutted by fire.
On its own, it means nothing, but when we learn that this is where he had his first date with his ex-girlfriend, and that he's now down in the dumps, become an alcoholic etc. because she left him, the restaurant begins to take on the appearance of a symbol. To make it more powerful, perhaps he is a property developer, and on a whim decides to buy the gutted building, and attempts to rebuild it and open his own restaurant.
When the story concludes, and he's moved on, perhaps found someone else, the restaurant is rebuilt and doing well ... the restaurant has now become a life symbol.
The important part here is that the restaurant has meaning to the character, and thus has meaning to the reader. Don't fall into the trap of just inserting symbols that have meaning only to the reader. These are generally not worth your time and effort.
So, if you want to reduce confusion, I would make sure that your symbols have meaning to the character(s), rather than the reader. Limit your symbol(s) to a specific goal, too. In my case, the restaurant was symbolic of the man trying to piece his life back together.
