Just apply to the same schools that you both like (enrollment in fall). The school will take into consideration that you are a couple. Also, it shows commitment and may boost your chances.
Kellogg and Chicago GSB are also in the same city (Chicago, of course). One of my
schools in the same cities: UCLA & USC, Columbia & NYU, ...
I fully understand your situation. A friend of mine is studying in MIT while his wife is in Rochester. So it takes a few hours for him for meet his wife.