I'm afraid to say, if you see bubbling above the sill cover, it WILL have spread under the paint behind the cover as well.
In hindsight, I would have saved up and let a bodyshop do it. Mainly because rattle can paint is NOWHERE near as tough as proper bodyshop stuff, and neither is DIY preparation unfortunately, which is key to preventing it coming back.
Thing is though, DIY repairs are fine to eek a few more years out of the old girl but if you want it gone for good, I'd recommend letting the pros do it because it's virtually impossible to get the finish right on that thick rubbery paint VW use.