its really simple - for the bottom sill, first verify its not corroded to the point of holes, use a hammer to check it, If it punches through you need to get new pieces welded in.
If its still solid get some sandpaper and scrub the rust off, then get a painter to spray some primer on it and let it dry, then mask off the panel till the upper edges only with tape and apply a heavy coat of undercoat to it, It wont rust again, while there if you look through the rear wheel opening you may find a few rubber plugs, Those are provided to spray wax into the body cavity to prevent rusting inside out. Those holes are the access to the entire run of the panel. A very long wand type tool is required for this.
The rubber undercoat on that part is actually the correct way, if you look at european built cars - they are like that because there is a huge rusting problem in the entire of EU.