Hyphenation is a real problem for writers. There are so many rules, and sometimes no consistency to them. The best advice I can give you is to get a CD of Merriam-Webster’s Collegiate Dictionary, 11th Edition, and download it onto your computer. I use it all the time, every day, as it is the accepted authority in book publishing. (Note: The CD is included in the paperback book in the back, so this way you will have the book as a reference too.)
The Chicago Manual of Style takes precedence over M-W, though, so I encourage you to download this CMOS Hyphenation Chart from CMOS 16th Edition, print it out, and refer to it whenever you are unsure whether a word should be hyphenated or not. Often CMOS will refer you to check M-W for their take on a particular word, so you need both tools. With both of these resources at your fingertips, you will be able to go through your book and clean it up. Remember—your spell-checker will steer you wrong a lot! It will often tag some words as not being in the dictionary when they are correct, and it will sometimes let a misspelling slip through, so use your spell-checker judiciously!