[OS X TeX] problem with running project root file

[Sheetal Silal]

I'm compiling my thesis in TexShop and set up the main project file. I didnt know that one isnt supposed to include \begin{document} and \end{document}. So when I typetsetted the main file, it reduced my chapters to this
\relax 
\@setckpt{Chapter2/Epidemiology}{
\setcounter{page}{1}
\setcounter{equation}{0}
\setcounter{enumi}{0}
\setcounter{enumii}{0}
\setcounter{enumiii}{0}
\setcounter{enumiv}{0}
\setcounter{footnote}{0}
\setcounter{mpfootnote}{0}
\setcounter{part}{0}
\setcounter{chapter}{0}
\setcounter{section}{0}
\setcounter{subsection}{0}
\setcounter{subsubsection}{0}
\setcounter{paragraph}{0}
\setcounter{subparagraph}{0}
\setcounter{figure}{0}
\setcounter{table}{0}
}

Does anyone know of a way in which I can get my chapters back? Any help would be much appreciated.
Also, are the packages and the begin and end document  only to be included in the project file and not the individual chapter files?