In 1996, I wrote an article intended to answer questions such as yours. Recently I revised and up-dated it. Rather than attempt to answer your question, and repeat myself poorly, I suggest reading the article, Basic Guitar Setup 101. If you aren't too interested in the theory on intonation, you can skip the last 20 pages.
Even if you don't do the work yourself, it will give you some insight into what someone you take it to will likely do. If you have any questions regarding the article, I'll be happy to try to answer them.
The article is located here:
http://charlestauber.com/luthier/Resources.html