Starting a PhD; Any guides to setting up a 'system'?

• Universities normally have poorly written guides and badly designed template requirements. Most of these are remnants of solutions to problems caused by typewriters. If your University does not have one and you are free to use your own style consider yourself lucky.

  Start fresh from a good base class. book, memoir or koma and modify as you need.

• Use a version control such such as git and a central git server such as github early in the writing cycle.

• Write clean tex files. See, for example Will Robertson's Github page, which I recommend you use as a guide. You can also find a lot of information here at tex.sx (e.g., see Writing and managing thesis in LaTeX).

• Last but not the least, start typing your thesis immediately. When I wrote mine I had two extra files, one called journal.tex and another todo.tex, but that was a long way ago and there are better ways for this sort of thing now. Currently at work I use a localhost with a wordpress installation for these. I also use Jabref for managing references.

As my late professor used to say "... anyone that writes a thesis using LaTeX deserves a PhD for this alone", good luck!

To build on Yiannis's answer:

• Use Git and comment prodigiously. It's always nice to know why you added something (e.g., "added section on blabbidy blab because Prof X wanted it there.")
• Consider splitting chapters/sections/thoughts into separate files and use the \input{file} function to combine them in one main file.
• Early on, find a good bibtex solution and learn to use it.
• If you're on a Mac, get to know TexShop, as it is awesome and will make things much easier.
• I put all my figures in a images/ folder to make things cleaner. You could consider using subfolders to organize even more according to your personal level of OCD.
• Use the todo package to keep track of what you need to do. You will end up with LOTS of notes to yourself; keep track of them somehow.
• This may not be a great idea, but consider never delete anything. Even with version control. Just add a \begin{comment}, \end{comment} block around text you decide not to use. You may come back to it later. Alternatively (and probably better), find some way of keeping track of your snippets of text... chances are, if you spent time writing it, you will be able to make use of it, if not now then later.

Thought I'd chime in here with a piece of surprisingly unmentioned yet super-critical advice. I strongly suggest you coming up with at least two backup plans. Hard drive failures and laptop thefts will set you back to the stone age the week before you hand in your dissertation. I'm a 3rd year PhD chemistry student. I manage our lab's computer cluster on a daily basis yet even I was dumb enough not to perform a backup in nearly 8 months only to be hit with a primary drive failure only 4 days ago. Thankfully I didn't lose any of my actual thesis stuff as I have a Dropbox account linked to 3 computers. With 2GB of space, this should be more than enough for any thesis plus revisions you may have to make (if you are using an unwieldy amount of high-res graphics), keep them backed up on some physical drives.

Backup your stuff at least once every week or two.