i've built all 3 houses and using them like this:
Lakeview Manor - real house with the kids, Mjoll and Lydia (library & alchemy)
Heljarchen Hall - the museum (trophy room and armory)
Windstad Manor - the store (greenhouse and kitchen)
thinking about allowing Ahtar to run the museum and i'll probably bring in Rayya to run the store.
My setup is
Lakeview manor: Full time home and my favorite, storage room, armory, and bedrooms for full house porch. Scenery is quite legit. Extra bedrooms so everyone has a bed.
Windstad manor: bedrooms, trophy room, kitchen. Love the view of solitude from bedroom porch!
The pale home: Fort home, all towers. Looks awesome! Might leave family there during dawnguard for extra protection.
Everything fully decorated. I love having all the top five heavy armors on display in my armory. Quite awesome looking.