When putting together a large document, LaTeX will help with some special features like index generation, bibliography management, and other things.  A much more complete description of specialities and enhancements possible with LaTeX can be found in the LaTeX Manual and The LaTeX Companion.

Leslie Lamport. L A TEX: A Document Preparation System. Addison-

Wesley, Reading, Massachusetts, second edition, 1994, ISBN 0-201-

52983-1.

Frank Mittelbach, Michel Goossens, Johannes Braams, David Carlisle,

Chris Rowley. The L A TEX Companion, (2nd Edition). Addison-Wesley,

Reading, Massachusetts, 2004, ISBN 0-201-36299-6.

LaTeX provides the basic facilities to work with floating bodies, such as images or graphics, with the figure and table environments.  There are several ways to generate the actual graphics with basic LaTeX or LaTeX extension package.  A much easier way to get graphics into a document is to generate them with a specialised software package and then include the finished graphics in the document.  LaTeX packages offer many ways to do this through Encapsulated PostScript (EPS) graphics, because it is quite easy to do and widely used.  

When working on a system with a PostScript printer available for output and with the graphicx package installed, use the following step by step guide to include a picture into your document:

Produce a bibliography with the thebibliography environment.  Each entry starts with \bibitem[label]{marker}

The marker is then used to cite the book, article or paper within the document. \cite{marker}

For larger projects, you might want to check out the BibTeX program.  BibTeX is included with most TeX distributions.  It allows you to maintain a bibliographic database and then extract the references relevant to things you cited in your paper.  

A very useful feature of many books is their index.  With LaTeX and the support program makeindex, an index can be generated quite easily.  

To enable their indexing feature of LaTeX, the makeidx package must be loaded in the preamble with \usepackage{makeidx} and the special indexing commands must be enabled by putting the \makeindex command in the preamble.  The content of the index is specified with \index{key@formatted_entry}

When the input file is processed with LaTeX, each \index command writes an appropriate index entry, together with the current page number, to a special file.  The file has the same name as the LaTeX input file, but a different extension (.dix).  This .idx file can then be processed with the makeindex program: makeindex filename

The makeindex program generates a sorted index with the same base file name, but this time with the extension .ind.

The tricky problem when customising headers and footers is to get things like running section and chapter names in there.  LaTeX accomplishes this with a two-stage approach.  In the header and footer definition, you use the commands \rightmark and \leftmark to represent the current section and chapter heading, respectively.  The values of these two commands are overwritten whenever a chapter or section command is processed.  

The verbatim package is basically a re-implementation of the verbatim environment that works around some of the limitations of the original verbatim environment.  The verbatim package provides the \verbatiminput{filename} command, which allows you to include raw ASCII text into your document as if it were inside a verbatim environment.

Most LaTeX installations come with a large set of pre-installed style packages, but many more are available on the net.  The main place to look for style packages on the Internet is CTAN http://www.ctan.org  Packages such as geometry, hyphenate, and many others are typically made up of two files: a file with the extension .ins and another with the extension .dtx

Once you have copied the package files onto your machine, you still have to process them in a way that:

Most web pages you find today are written in HTML.  This format has two significant disadvantages when writing scientific documents:

The creation of a PDF file from LaTeX source is very simple, thanks to pdfTEX which produces PDF output where normal TEX produces DVI.  There is also a pdfLaTeX, which produces PDF output from LaTeX sources.

To produce a PDF instead of DVI, it is sufficient to replace the command latex file.tex by pdflatex file.tex.  

pdfLaTeX can deal with all sorts of fonts (PK bitmaps, TrueType, PostScript type 1...) but the normal LaTeX font format, the bitmap PK fonts produce very ugly results when the document is displayed with Acrobat Reader.  The Type 1 font set most widely used today is called Latin Modern (LM).  

Two ready-made font sets are available for this purpose: pxfonts, which is based on Palatino as its main text body font, and the txfonts package, which is based on Times.  To use them it is sufficient to put the following lines into the preamble of your document:

\usepackage[T1]{fontenc}

\usepackage{pxfonts}

Including graphics into a document works best with the graphicx package: \usepackage{xcolor, graphicx}

The bad news is that graphics in Encapsulated PostScript format do not work with pdfLaTeX.  If you don't define a file extension in the \includegraphics command, graphicx will go looking for a new suitable file on its own, depending on the setting of the driver option.  For pdftex this formats .png, .pdf, .jpg, and .mps but not .eps.