I have the same issue - a paint chip on the roof that has rusted. Do you need to do anything before using the paint touch up pen? I was thinking of getting one of the 2 way pens where one side is the paint, the other is the clearcoat.

Do I just apply the paint over the rust spot, let it dry, then apply the clearcoat?

Thanks for your advice - I know nothing about paint/detailing.

Pick up a prep pen sanding stick and get rid of every trace of rust. Make sure you get all loose paint as well. Then use the touch up paint.
The roof panel is very obviously not treated for rust resistance the same as the lower body panels. I have a major chip on the front fender that after 4 years and salty winters has some minor surface discoloration on the steel. I have 5 chips along the front of my roof that look like a 20 year old car already.


https://repaintsupply.com/images/products/47569.jpg

I have some old IronX from when I used to work near a rail yard and was fighting fallout daily. If you can get some of that to knock out the rust before you apply, that's what I did. Then you can keep it around and detail a couple times a year with it. Much easier than claying. Also my method involves getting a dab of the paint on a piece of paper and applying with a toothpick. Once it dries too much make another small dab. Let it settle each time before you apply another layer. Unless you would rather over apply and then sand down with a circle of fine grit sand paper glued to the eraser tip of a pencil.