Assuming you're referring to the uses for them that I think you are (and as someone who tends to use them a lot for purposes like these), here's a few links that help me remember when to use them and why.

Rules and examples for:
Parenthases (http://www.grammarbook.com/punctuation/parens.asp)
Commas (http://www.grammarbook.com/punctuation/commas.asp) — Rules 8, 11, and 20
Dashes (http://www.grammarbook.com/punctuation/dashes.asp) — em dash is the one you want, though it's good to know the difference between the two kinds.

Also, a manuscript is the book you want published. Once you've written your book and are satisfied with it, you print it out and mail the printed pages to the publishers. That's your manuscript. If you want a more...dictionary-type definition, Merriam-Webster's site has this to say:

1 : a written or typewritten composition or document as distinguished from a printed copy; also : a document submitted for publication
2 : writing as opposed to print