I haven´t tried to add the controller to an existing w2k installation so i´m out of experience there, but the manual are quite straightforward on that issue: Install the drivers, shutdown add yur controller and then boot.
As said, i haven´t tried that but installing w2k clean with the controller attached isn´t any problems at all. Just press F6 in the beginning of the installation process (when you are given the option) and then put in the diskette with the drivers and it works. just as simple as that, no problems.