Well, right, you do want to install a new dash (I'd recommend Unleash over EvoX, but do whatever is easiest to get started) so that you can launch apps play games from your hard drive, and all of that good stuff.
But that dash will not be replacing the MS dash. If you are using the stock hard drive, the MS dash will remain intact. You will have two (or more, if you want) dashboards.
So when you boot to the 5035 bios, you will boot to the EvoX (or Unleash or XBMC or whatever) dash. But when you boot to the retail bios, you will boot to the MS dash, and you can log into and play on Xbox Live.