Looks like you have metal flaking off. Rust will just keep coming back. If you are keeping the truck for a while the best thing to do is have a body shop cut panel and replace. Don't let them just weld over, they need to remove back to no rust, weld flush metal to flush metal, then sand down weld seem, should only need thin coat of body filler. You also need to rust proof behind the repair as it will have bare metal.
Another option is to sandblast and grind, prime and paint, then get plastic sill guards and install over. You will see rust again within a year, just how it is. Sorry to not have better news, good luck with whatever you do.