The better way, in my opinion, is to cut out the bad bit and replace it.
Bruce at Blue Star Garage sells a repair section that has all the internal gussets to replace the bad/rusty section (
Rust Repair | bluestargarage).
His instructions are super-detailed and he include 95 photos of the process. Send me your email address and I'll send you the photos if that helps.
I have bought a few of these pieces for my cars but I haven't done the repair yet.