As I mentioned previously, I am writing my thesis using the LaTeX markup system, and thought I would put together a few words on my experience and things I have found. This includes formatting tables, including acronyms, and larger landscape figures/tables. I am sure there are many other ways to to achieve the same result, but these are the ones I have found to work.
Whilst I have not been at this research malarkey very long, several people have made suggestions for useful software, in addition to my own past experience. I have put some notes/links below on various tools that should help towards the process of research. Hopefully this might be of interest to others, and feel free to add your suggestions below.