The best bet is to have them welded up.Filling them with body filler caan cause problems later with rust forming form the back side. Craig Hager tech1@chevyduty.com
I agree with welding them closed. Use a copper spoon available from Eastwood to back it up and absorb any excess heat. A decent 115VAC MIG welder will be more than adequate to do the job. I've had extreme success doing the same thing with my Lincoln SP-170 MIG welder cranked down to a suitable setting. .025" wire with a 25% CO2/75%Argon shielding gas is ideal for such a job.