Watching their demo video on their site, they use the rust barrier on rusty metal without a primer. Knock off the rust and hit it with a grease and wax remover and apply directly over rusty metal.
From your pictures you were way ahead of what they were doing so I would say you are good to go.
Some of the paint guru's may chip in and say otherwise tho.
oh, no wait... it's totally messed up and I will gladly take it off your hands!
