Your school may have a LaTeX document class and/or package file that you can use. Many of them, especially large public schools, do. If not, my guess is that you'll be best served using report rather than book, since most schools still require theses and dissertations to be single-sided (as in report), not double-sided (as in book).
You can input the chapters however you wish. I personally used \include{filename} for each chapter, which automatically starts a new right-hand page for each chapter. You can use \input{filename} instead if you don't want TeX to clear the page first.
As for the cover page, that has to do with chapter formatting. If you want that in addition to the standard chapter heading, then I might suggest looking up the definition of \part and trying to tweak it to your needs. I don't know a package off the top of my head that does what you want to do, but others might.
