Hi Graham,
The captive nut retaining channels replace existing ones that don't have the plate with the nuts on - so its just a case of unbolting the old and on with the new. However, in my case, the captive nuts didn't quite line up with the holes in the bodywork - they were a bit lower, so I solved this by making a couple of shims out of 2mm ali and putting that below the retaining channels. There's more than enough stud sticking up to do that.
Yes you need to remove the knee protectors mine are fitted with black self-tappers which you might want to use when refitting just in case you want to get in there in the future. There shouldn't be anything else to remove.
Hope that helps,
Jonathan