Treating rust and touching up paintwork

[ellectrastar]

Have just bought a five-year-old Ford Transit and have noticed the obligatory rust patches, two or three spots, probably the size of a 10p. When you open the van door, it's on the underside of where your side compartment is, so it's not too visible but I want to make sure it doesn't spread etc. Can someone advise the correct procedure to deal with it?

I've had a look online and seems that I need to use an abrasive to rub away the rust - would this be a sandpaper or wire wool? It says to do this until I can see clean metal. Then wipe the area clean of dust and use a primer, paint, and clear coat. And then buff.

As it's under the door do I need to worry about the primer and clear coat?

I am aware the van side door has had a respray as I was told there were scratches all along it. Fair enough as it was a commercial van and they don't always get respected! Around the door handle (like mostly underneath) the paint is a little flaky. I want to put a bit of touch-up around that as well so it doesn't all just start peeling off, but again it's not too visible so what is the best thing to do with that?

Many thanks for any advice.