I don't have a Raptor, but it should be similar. Some RV skylights have screws on the interior side of the RV, if so those naturally need to be removed. After removal, go on the roof and scrape off the putty or caulking from around the base of the old skylight using a plastic (I remove the sharp edge with a bit of sandpaper) putty knife. Work gently with the putty knife to avoid damaging the RV roof, patience is needed for sure. Now remove the screws from around the base of the skylight and pull it out.
Now, more putty
or butyl tape is underneath where the skylight flange was. If there is, remove it. Do this carefully, as your going to start pulling even more at your rubber roof. Clean along the edge of the exterior area of the skylight hole, underneath (everywhere) where the skylight flange was, with a rag and isopropyl alcohol.
Place new butyl tape along the edge of the skylight hole, over the pre-drilled screw holes, where the new skylight flange will sit or if using the same type and style, then the existing holes should be just fine, placing the screws inside the pre-drilled holes on the skylight flange through the pre-drilled holes in the RV roof, again, unless you are using the same style that came with it. Make sure you remove any of the butyl tape that is visible around the edge of the skylight, be careful, keep in mind the rubber roof.
Now for the self-leveling butyl rubber caulk (Dicor) around the edges of the base of the skylight to create a seal to prevent water from leaking into the RV.
Don't forget to now go back inside the RV and replace the screws on the interior side of the skylight unless you have a new one that don't need those screws.
If by chance (and I have not heard that, but....) they are on with staples, after scraping off the existing Dicor, just pull the staples.