As far as I can remember - yes, it will try to overwrite your Python dir, at least it did for me on my Windows machine (I backed up my original C:\Python27 before trying EPD, and then had to restore it, IIRC; there was also some mess with paths, but nothing incurable). I also tried installing EPD into its own directory, but Windows EPD package failed to run Notebook anyways (some issues with Tornado), and I was just too excited to try Notebook. Jumped to Ubuntu@EC2 and was running Notebook with EPD from it in 5 minutes.
Your mileage may vary, of course, so I'd say have a backup and give it a try - at least EPD didn't ruin anything for me. I'm pretty sure IPython Notebook on Windows machine is doable with some lib-hunting/building, since I managed to have fully functioning IPython Qt console installed and running perfectly on Win7 right now, and Notebook is just a couple additional requirements away from it.