After writing the book, this is the second hardest work. After your book goes into production, you will work with an editor, and two kinds of editing happen next.
a. The first is basic copyediting. Your publisher will either hire or have an in-house copyeditor read and mark your manuscript. This will generally include grammar, punctuation, and general sense notations. Depending on the shape your original manuscript was in, there may be many or few marks. You have some rights here--that is, you can basically keep your manuscript intact if that's what you want. But copyeditors are professionals, and you must at very least understand and think about what each mark is suggesting.
b. Also, this is the time to make changes if you need to. If you've revised something, or rethought it, making changes now is appropriate and doesn't cost anybody any money. This will not be true later. But be sure to talk this over with your editor.
ADVICE. Copyeditors are not there to change your work. Their job is to be sure that you are saying what you think you are saying, and that it's being said in the best way possible given the context. It is true, however, that copyeditors may not always get the point you are making--they are not, after all, the author. But if they don't get it, think about the implications of what that means. After all, they read books all the time. Can you say what you're saying a little more clearly? This is a real question, and one you must address. Do not immediately blame the copyeditor.
c. The second part of the editing cycle will be when you look at the galley proofs. This will be your manuscript, again, but now set into type as if it were a book, though it will be unbound. It's your job--and your joy--to look through the manuscript again, looking for errors of any sort. Now, however, is not the time to make changes. Changes in the manuscript at this point will cost money. While publishers will certainly change anything in which they are at fault, they will not cover any kind of substantive changes. If you simply must make changes at this point, you will assume any and all costs regarding that change.
ADVICE. Some minor changes may be negotiable, depending on your publisher, but the best thing is to have made all changes when you had the chance. This assumption of liability for changes will probably be in your contract. You have been warned. Oops or I'm sorry don't go very far at this point.