well for instance you could do this matrix style. Neo can see the world as numbers. So if you already have the city done you could apply some filter to make it look like you are moving in the cyberspace. The netrunning would boil down to finding some things in this new world while figuring out how to deal with certain obstacles. You could even bend some rules of the reality (again like in matrix) but the problem with the obstacles is - few agents Smith wouldnt probably do the job. Therefore a need for something more clever.
This.
They could strip the actual city from it's external layers and leave just a "skeleton" of buldings, streets etc while adding elements specific for netrunning.
And about moving - after leaving the cyberspace you would end up in the same place as you started netrunning, simple as that.