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LaTeX formatting - basics

I am virtually clueless in the world of LaTeX. Having said that, I'm liking it a lot due to the power with which you can create fantastic looking documents; even if the learning curve is rather steep.

Below is an approximate layout (with the actual text removed) of my final year project at university:

%Preamble.  Ths stuff is important!
\usepackage[sort&compress,super,comma]{natbib} %required for bibliography
\usepackage{subfig} %required for figure layouts
\usepackage{textcomp} %required for celcius sign which is typed using \textcelsius
\newcommand{\ul}{$\mu$l} %Example, type "\ul\ to get a micro-litre in text, 
                         %rather than typing it out every time.
%End preamble.

%% F L U F F %%

%Double spacing is looked down upon by many, but a lot of academic documents want the space 
%for markers to write comments, so we have to use it!
\setstretch{2.0} 	%default spacing to be double spaced. To change from this, use:
			%begin{doublespace} end{doublespace}
			%begin{singlespace} end{singlespace}
\title{Title here}
\author{Name here}

\pagenumbering{roman} %use roman numeral numbering for intro stuff

Put your acknowledgements in here

% NOTE: lines longer than a page width do not work nicely here by 
%default (no wrapping apparently)
% How-to for table: The ``&'' separates columns, and ``\\" indicates the end of a line.
% More information on how-to with tables is 
    Cell A1 &  Cell B1 \\
    Cell A2 & Cell B2
%End of Abbreviations

%% M E A T %%

An abstract would go here
\pagenumbering{arabic} %get proper numbers for pages from here on in

%%%%%%%%%%%%  I N T R O D U C T I O N %%%%%%%%%%%%
\linenumbers  %Useful for when you're editing(but not in the final document), as this puts linenumbers in

\section{Introductory introduction}
Using a bibtex file (I like using Kbib for this as it can search pubmed to import
references) you can reference items in the file by it's "key" by typing \cite{key} and it will reference in the text correctly, and construct the bibliography as indicated at the end.

\subsection{Referring to figures}
I wish for you to see fig.\ref{fig: short-label}

%%% Single figure
 \caption{Caption goes here, including references or citations\cite{Wikipedia2008})}
 \label{fig: short-label} %short label here so that we can refer to it in the text by it's figure number

%%two images/figures next to each other
    \caption{Captoin information}
    \label{fig: label}

%% Numbered list
 \item Item 1
 \item Item 2
 \item Item 3

%%%%%%%%%%%% M E T H O D S %%%%%%%%%%%%%%%
\chapter{Methods \& Materials}

This is top
This is a section of above
This is a section of the one above it
%%%%%%%%%%%% R E S U L T S %%%%%%%%%%%%%%%


%%%%%%%%%%%% D I S C U S S I O N %%%%%%%%%%%%%%%

%%%%%%%%%%%% B I B L I O G R A P H Y %%%%%%%%%%%%%%%%
\newcommand{\bibpreamble}{References in the style of Nature} 

%%%%%%%%%%%% A P P E N D I C I E S %%%%%%%%%%%%%%%%
\chapter{Appendix 1}
Use if needed.