The first thing you need to do is check with the building department to determine the zoning and building limitations and requirements. Then I would recommend you hire an architect or at least an architectural draftsman to come up with some conceptuals.
As a general contractor, real estated broker and developer I would have to tell you that you question is far to open ended to answer on a real estate comment thread. You may want to probe a contractor or architectural forum to get a more concise answer to your question.
Rule of thumb, howver, going up will add roughly 50% to overall construction costs. But that said, since you're going up over a garage which is by and large only a shell with very little if any infrastructure i.e. gas, electric, plumbing, etc. the cost of a 2nd story garage apartment would probably be double or more since I'm assuming you would want at least a bathroom included.... more