Ok say I get married but I own two houses do I get to choose which one she lives at? Also if I own a home in say Markareth but my wife is from Windhelm will she open her shop where we live or in her town?

Yup, it will be in her dialogue. Tell her you want to move, where and that is where she will be. Now if you could get Two Guys And A Truck to move all your stuff between the two.

Ha ha ha ha

Can I move her between homes or once I pick I'm stuck