are your side skirtd urethane or fiberglass? if they're fiberglass, you're kinda screwed, because the cracks will come back. the only way to fix them is to cut the crack out, and use fiberglass to repair the crack. if they are urethane skirts, filler would have just cracked and fell off if they flexed. the best you can do with those is primer, sand, reprimer, resand and so on. as for the paint, to not sand the color. wet sand only the clear coat, CAREFULLY, with 1500 grit wet/dry paper, nothing lower. then buff with an electric or air buffer and the proper buffing compounds.