I just recently transitioned my site over to WordPress, and I must say that the process, though it may seem tedious at first, is well worth it. What I do suggest you do, however, is not touch your main site until you’ve completed the turnover process in it’s entirety. What I am suggesting then, is that you make a second copy of your site, or at least the main files and move them into into a folder, ie: mainsite/blog/ and edit new copies there. Once you are satisfied with what you have there, moving your newly created WP site to the main diretory is simply dragged (or copying, in the case of Linux) your files over the old ones and change one or two options in the settings of WP.
