|"If I add this controller and the second hard drive will I simply be able to connect the existing hard drive and boot the system back up without having to do anything to the actual existing Windows installation."|
It will not boot once you have moved the windows drive to the raid controller.
There are a number of factors to be considered.
First is you should get two exact same drives for the raid controller. You can't just mix drives in a hardware raid array.
Next, to have a fail back plan, you would clone the existing windows drive to one of the new ones in the raid array.
Then you would do a repair install of 2000 at which time you add the raid controller driver.
Note: make sure the controller supports 2000!
Then once its booting and updated go into the raid array and mirror the drive to its shadow.
If something goes gunnybags during the process you can fall back on your previous drive setup to be operational.
BTW you should have a second DC so if the first one fails you can rollover to it with no issues beyond seizing some FSMO roles.