I definetely reccomend using Latex. It is easier than you think to learn it, and once you use it you probably never go back to word. Plus, most of scientific Journals have their own templates for submiting papers, which I assume will take a lot of time to adjust to ms word yourself.
For PhD templates I use one that I found from MIT University (although I do not study there).
MS Word is still the best one for writing such huge word documents. Because of the newness and related anxiety is still in using Latex. Moreover, it has to be installed as and when required. Not only that, its in its infancy stage of development and compatible only with Windows 7. MS Word is compatible with any operating system of any time. For repairs and maintenance, only remote possibilities available. With all these bases, i recommend MS Word only for Ph.D Thesis writing. As, it is a continuous and laborious documenting work, it is risky to choose other modes of operations than ever available resources. Hope my answer is clear and helpful. All the very best..!!
Thanks! I have finally chosen Latex for thesis writing and submitted my thesis. I think I would recommend Latex over MS Word for Thesis writing :) Latex is much better than Word for research paper or Thesis writing given that you have a template available. For project report or few pages report writing, MS Word is easier to handle.