Either way is fine. The first method has the advantage of addressing all the rust at once, in one shot. The other way you are addressing the rust, just more at your pace. If you go the second route (that's the way I go) then the biggest thing is to make sure you are very thorough about dealing with the rust. The goal is to stop the rust, fix the damage, and prevent future corrosion. Which way you want to go is entirely up to you.
