if you haven't tried it already, try seating the stiffer side of it first (the one with more material) and then popping the more flimsy side in. or vice versa...i wish they made those things out of a softer rubber, rather than the hard plastic.
i don't use them. they only serve to make the bar/brakes look "cleaner," (i happen to think it makes them look janky) and are, as you've exerienced, a pain in the ass to install. i'll usually try only a couple times to get them in (sometimes they go in no problem) before i pull the whole thing apart again and take them out. the cable housing won't wear away at the clearcoat on the carbon, because in most cases, the housing is softer than the clearcoat, and the housing also isn't usually going to move against it as you turn the handlebars. so there's no danger in not using them.