No difference at all between the 96-99 and 99-00.
I have skirts from a coupe on my hatch. You need to trim about an inch or 2 off and drill new mounts. You can file out the stock mounting holes so the EK clips fit in but I just used self tapers and have had no problems at all. I measured my stock skirts and then marked the EK ones and cut them with a dremel.
You'll have a small little gap close to the end of the door and you'll have to make some end caps.

If you have a 4dr be sure to get 4dr skirts. If you have a coupe or hatch get coupe or hatch it doesn't matter which.