Update for MikTeX 2.9 below.
I've been working on my thesis for a couple of months now, and frequently I have to look up ways to tweak certain Latex components, so I'm going to start posting about these tweaks, even if it's just to link to another page about how to do something. If I end up having a good collection at the end of my thesis, then I can write a final post aggregating them in a logical order so they can serve as a guide to formatting a thesis in Latex.
I'm using TeXnic Center (TXC) 2 Alpha 3 to edit and MikTeX to build. I originally installed both using ProTeXt which packages TXC1, MikTeX, Ghostscript, and Ghostgum. I later installed TXC2 which provides a much-needed overhaul to the interface so that toolbars don't shift all over the place whenever you resize the window.