These instructions were copied from the HOW-to included with the MR1 update...so ALL credit goes to the person that included them with the MR1!!! 
ROM Upgrade Utility (RUU)
Before Running the ROM Upgrade Utility
Before you run the ROM Upgrade Utility (RUU), make sure you check and do the following first:
1. USB sync cable is connected to the computer.
2. The standby and hibernation modes are disabled on the computer.
3. All running applications on the computer have been closed.
4. USB sync cable is connected to the Mobile Device.
5. Do not interact with your Mobile Device unless instructed to do so.
General Procedure on Installing the ROM Update
The upgrade process takes up to 10 minutes. It is recommended that you close all programs on your PC prior to starting the update program and do not open any applications or files while the update is in process. All customization and downloaded applications will be lost however contents of the SD card will remain intact.
1. Back up your personal data from the Mobile Device to your computer using HTC Sync if you want to ensure you don

ROM Upgrade Utility (RUU)
Before Running the ROM Upgrade Utility
Before you run the ROM Upgrade Utility (RUU), make sure you check and do the following first:
1. USB sync cable is connected to the computer.
2. The standby and hibernation modes are disabled on the computer.
3. All running applications on the computer have been closed.
4. USB sync cable is connected to the Mobile Device.
5. Do not interact with your Mobile Device unless instructed to do so.
General Procedure on Installing the ROM Update
The upgrade process takes up to 10 minutes. It is recommended that you close all programs on your PC prior to starting the update program and do not open any applications or files while the update is in process. All customization and downloaded applications will be lost however contents of the SD card will remain intact.
1. Back up your personal data from the Mobile Device to your computer using HTC Sync if you want to ensure you don