weld up the holes.
I found that placing a copper penny on the backside of the hole and then using a couple tacks with the MIG right up against the steet metal will fill up the hole nicely. Don't get too much heat on the penny though because it will melt and polute your weld (learned that the hard way). The penny just creates a backing so that the weld puddle distributes laterally on the panel rather than into it.
If the holes are too big for this method, you can just put a scrap piece of steel on the backside of the hole and now plug weld your panel to it. If you go this route, use a weldable primer on your scrap steel. It also is good if you can access it and get some seal sealer around it afterwards.
Not sure if these are the best methods or not but they work good for a begineer welder/bodyman such as me.