I didn't remove any decals when I fitted mine, I'm not sure you actually can. There are also some parts of the kit which duplicate the protection already on the bike, I left those off and kept as spares, apart from the down tube so it gets double protection.
I left all mine on. This left a very fine line around the edges of the factory film but I was able to minimize that by slightly heating the area and running a credit card along those places to force the new film onto the frame closer to the edge of the factory film. I figured doubling up the protection in those places was more useful to me than a slightly smoother appearance. The Specialized logo on the downtime is much more subtle on my black matte comp after covering it with the satin ppt film but I actually like that look better.
I used ridewrap took off all the factory frame protection down tube and around rear triangle, bike was easier than last I did i have the oak green 21 and used a matte kit has turned out good has little shine to it over stock finish