easiest and fastest is to tap a small dent with body hammer over hole.pop rivet the proper size peen it slightly after grinding it flush and filling with bondo.i did this on a vinyl top holes.done properly it is a permanent fix
There's a couple options... first, bondo(don't recommend this one), second, a copper spoon if you can get behind it and simply fill it with a weld pool, third, make little circle patch panels and weld them up.
This. A copper spoon and weld it up. For larger holes you can make a little patch, but for the holes in questions I'd just back them up with a spoon and weld them up.
Bondo should NEVER be used to fill holes. It's not waterproof, it will in fact absorb water if not completely sealed. Using it to fill a hole pretty much always results in the hole rusting out from the backside, leaving a much larger hole to fix when the bondo falls off.