The Clear Coat on my Son's El Camino (roof) is peeling or lifting. Water is being trapped underneath and spreading. How can we stop this and/or repair this ???

Short of sanding / preping and re-shooting the offending panel, I'm afraid your left with living with it.
:dontknow: But hay what do I know.

???? ~ You also didn't say if the paint on the Veh. is the Orig. (77), or if it has been re-painted at some point in time.
If it's Orig. 30+ years old, It could vary well need a New entire Paint Shoot anyways.

I also think there`s no other way to paint it new!When the clear coat get some cracks or it`s "brittle",water comes between clear- and paint coat,and that looks a kind of milky!You can also find that at aluminium rims...

Once you get clear coat failure that's it, no way to repair it. It needs to be removed and re-shot.