The story I can most remember setting in a city I was only marginally familiar with was NYC. And the story was for a prompt that specifically asked for a big-city SPN casefic, preferably NYC. (I had been a tourist there but hadn't explored the residential neighborhoods, certain churches I wanted to use, etc.)
Besides all the other great comments you've gotten here, I have a couple more suggestions. One thing I did was rent some movies to scrutinize that were set in that city. (For NYC, that wasn't hard. Not sure if that's an option in your situation.) And the other was to solicit input from folks who lived there, ask for descriptions or anecdotes that can add a you-are-there quality to the story. (Again, maybe that's not an option in your current dilemma.)
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Besides all the other great comments you've gotten here, I have a couple more suggestions. One thing I did was rent some movies to scrutinize that were set in that city. (For NYC, that wasn't hard. Not sure if that's an option in your situation.) And the other was to solicit input from folks who lived there, ask for descriptions or anecdotes that can add a you-are-there quality to the story. (Again, maybe that's not an option in your current dilemma.)
Good luck!