To rid the house of urine smell you will need some kind of enzymes. What you are smelling is the waste products of the bacteria and other microorganisms that are eating away at the urine. Their waste is mostly made up of ammonia, hence the bad, potent smell. Left to itself urine will break down over a period of years. Using enzymes will speed up nature and do it much faster.
You didn't mention what type of floor your dog marked, but avoid vinegar or anything acidic on carpet. Most carpet is dyed with acid dyes so using vinegar can sometimes set in stains.
Every urine case is different, so the only way to guarantee complete odor removal would be to remove or clean everything that the urine contaminated. In the carpet world that means tac-strip and carpet pad is replaced, your sub-floor is sealed, and your carpet gets cleaned on both sides. A very involved process that can be fairly pricey.
Using enzymes will be cheaper and easier, but you do need to get the enzymes in contact with everything that is contaminated (on carpet a small spot on top can be 4-6 times larger underneath. It is also important to know that every enzyme product is different and just because one product doesn't work, doesn't mean another won't (most enzyme products only contain 6-8 different enzymes, before they start to destroy one another).
At Zerorez our enzyme product contains literally thousands of pro-biotic enzymes (meaning they promote oxygen producing, healthy bacteria). There really isn't a smell that it can't eliminate quickly, effectively, and safely. You can visit us online at: http://www.zerorezdallas.com
If you are interested in just purchasing some of our enzymes send me a message and I'm sure we can work something out to get you some of our enzymes.