I'd say first things first, you need to decide on two main things:
1) Are they carving out the whole thing, part of the thing, or constructing inside a natural cavern?
2) Are they a 'vertical' society or a 'horizontal' society (Shanghai and Manhattan are vertical societies, US and Australian Suburbs are 'horizontal')?
Then you can start designing the big ticket items.
Also, most cities start small then the reorganise around major buildings: Shopping, Law & Order, Government, Work, Defence.