Can it made in some way where the dogs can stay at your own house and just stay there and act like a house dog. Also when i make my dog wait some
where if i leave the area and come back he disappears back to his original home Vigilance(Markath Stables) Meeko(Meeko's Shake). Don't know if i'm the only one with this problem.

It's how the game is set up. There are currently no mods (for PC) to make the dogs stay at your house of which I am aware, but I'm sure as soon as the CK comes out that will be rectified.