Hell yes, you should have uninstalled the old 9800 driver before installing the 550! Then install the proper driver from the nvidia site for the 550. I am surprised it ran. When you get the 560, uninstall the 550 driver, shut down machine, pull plug from wall, push start button for 10 seconds to discharge the caps on the motherboard and video card, pull old card, install new card, boot up and install new drivers for the 560.
Doing a full install with the newer NVIDIA drivers does an uninstall/reinstall automatically. They added this in the last year.
As for the rest, I've never discharged the caps or heard of anyone damaging a board changing a video card, but erring on the side of caution is not bad advice.