With book class, you can do this:
thesis.tex
\documentclass{book}
\usepackage{geometry} %%% put packages you need here
\begin{document}
\begin{titlepage}
\vspace*{1in}
\Huge This is the title
\end{titlepage}
%%----------------------------------------------
\frontmatter
\include{acknowledgement}
\tableofcontents
\listoftables
\listoffigures
%%put nomeclture command here. I don't know the details of how you do it.
\include{abstract}
%%--------------------------------------
\mainmatter
\include{introduction}
\include{what} %% first chapter
\include{how} %% second chapter
\include{results}
\include{Conclusionandfuture}
\backmatter
%% like appendix if any comes here.
\end{document}
In \include{file name} the file name stands for the file name of your sub-tex files. For example your introduction.tex may look like this. I remember that First page of Introduction should be unnumbered.
introduction.tex
\chapter{Introduction}\label{chap:intro}
\thispagestyle{empty} %%% make first page with no page number
%
Some text here and your introduction starts which has sections
%
\section{some section}
Some text again....
.
.
.
And a sample chapter file:
what.tex
\chapter[What's this?]{What am I doing here?}\label{chap:what}
What are all these......
..
.
.
\section{Motivation}
Some text...
.
.
.
Put all thes .tex files in the same folder and compile thesis.tex file. You may prefer to put sub-files {what.tex, how.tex etc) in a sub folder for neatness in which case you have to use \include{subfiles/what} where subfiles is the folder that contains what.tex. Both thesis.tex and subfiles folder reside inside the same folder.
\frontmatter,\mainmatterto change page numbering style. – Reza Feb 03 '14 at 07:20memoirclass. I used this for my thesis and was very happy with it. I prepared a basic layout that I used for my thesis. Feel free to use and modify it. https://github.com/tdett/thesis-template. Also, consider learninggitormercurialfor version control. – Eekhoorn Feb 03 '14 at 08:48