Example Layout

The thesis can be roughly broken into 4 main groups, as shown below. Only the middle two groups count toward the word count. This is purely an example, you can modify the names of the headings as you see fit:

Cover Page - Project title, your name, the date. You may have a relevent picture. Perhaps your sponsors logos.
Abstract - Make this about 200 words long, and give a full overview of the project. Not too detailed, not too sparse. Oh and do it last. Education-line Guidance on Abstracts
Statement of Confidentiality - A compulsory sheet (pdf/docx). Read it, obey it, sign it.
Acknowledgements - You want to mention the companies that sponsored you and/or gave you data. Your supervisors. Friends, family. Pets. Just look at the old theses in the lab to see some examples.
Contents - Word and LaTeX can build this for you, and long as you set it up correctly. See the Word Tips.
List of Figures - Again, these can be automatically generated as long as you use the 'Caption' option in Word, or \label{} in LaTeX.

Introduction - Set the scene - You want the reader to be drawn into reading the following thousands of words, so make sure there's a clear focus to the project.
Literature Review - What have other people seen? What are you expecting to see? - This doesn't literally mean "put in the literature review you did at the start", it's a summary of the published literature in the area. Any models or key references you use in the discussion must be in here.
Data Used - What do you have to work with? - This is where you would give a summary of your (for example) seismic survey, how many lines? What's the coverage? Spacing? Think- this is information that would be really easy to put in a table or a figure.

Methodology - What did you do? - Don't use too many words, but use enough to give me a full overview of what you have done. A flow chart might be useful here. Make sure not to show your results (or, at least, keep them minimal and purely illustrative) as they will be shown in the next section.
Results/Observations - What did that make? - You'll want to think about how to structure this section, as you should follow that in the coming sections similarly. Usually you'll do this stratigraphically (start with the oldest and work up) or spatially (work from the centre outwards). Other projects may need you to show the results of each step in your workflow. Do not interpret what you see!
Analysis/Interpretation - What do you think it means? - This is when you can interpret your results. Which will probably feel like you're repeating yourself a lot, but in Word and LaTeX you can very easily refer back to images: "see Figure 4.5". Make sure not to compare it to literature, becomes that comes in your...
Discussion - What do other people think it means? - So using the models in you Literature Review, how does what you have observed and analysed fit into the current body of work? Is it the same? Is is different? How different? What are the implications?
Conclusion - Could you give me a quick summary? - Remember how in all the papers you've been reading you've skipped to the conclusion to see if it were worth reading the whole thing? Make sure you conclusion makes people want to read the whole thing. This is also where you can mention any further work that could come out of your project.

References - Make it automatically. Please. For you own sake.
Appendices - Data tables, extra cross-sections, enlarged or complete cross-sections, code. This can also be on a cd.