How should I go about ridding my whole house of the smell that makes dogs keep peeing?

How should I go about ridding my whole house of the smell that makes dogs keep peeing?
I have been using Natures Miracle to get rid of the spots immediately after he uses the restroom there. and from what I can see it is working but now he is peeing in places that he never would have looked at twice before I got rid of his old ones. So now its like I am having to clean the whole house with this stuff and its not the cheapest thing in the world either. I have already gone through one whole bottle in a week. I take him out side and he pees but its almost like he doesn't let it all out so he can save some for the inside to. I have tried treats and he will get it after the first time that day, but try it the next morning and he has forgotten all about getting a treat if you go potty. I have a little patio that I am debating on just turning into a dog restroom for him because a trainer said to put a napkin with pee and some poop on it in a spot and go there every time. and that with help train him.... problem is I live in an apt and the lawn guys get rid of stuff like that and plus there are too many distractions for him to concentrate on going. So my question or questions are 1. Is there anything I can do to treat my whole house (tile floors and an area rug) to get rid of "his" scent? So I can kind of start over in potty training and try to get him to learn that out side is better. And should I do what I was thinking of doing to the other patio? Will that confuse him if we are out somewhere else or when we move? Or are there any other tips or tricks that I can learn to make them start using the restroom outside?