I have never used the Raptor bedliner, so I don't know if it's a very hard / rigid product or a flexible rubbery one. The flares are polyurethane, and for best adhesion, you need to wash them with both hot soapy water and a solvent cleaner ( two rag system - wipe with wet and then dry rag before it evaporates on it's own ) before any sanding.
It's also best to wash them after sanding with soap and water as well as a specialty solvent for plastics. ( the one I use has stoddard solvent as it's main base )
If the flares aren't going to be removed from the truck, then you need to be careful that you don't have water trapped between the body and the flare that will come out when applying your bedliner.
I don't know how you intend on applying it, if rolling it on with a textured roller, I would probably sand the existing paint with a P240 / 320 grit. You might even be able to go coarser, p180 to blend any peeling paint. If you need to prime bare spots, for best results you want an adhesion promoter and a flexible primer surfacer, and follow the directions before applying the bedliner.
As long as the existing finish is in good shape, do not remove it, however I am sure that the lower portions will have bare plastic and rock chips. Blend the edges down of peeling paint and give the rock chips a once over.
Remove the screws around the wheel wells, and re-install them after you are done.