If they are rust holes, you will want to cut out the rust back to good metal and weld in patches. It is very tough to weld a good metal patch to rusty metal.
Cut the holes back to good metal and make your patch fit the hole and use a mig welder with .023-.025 solid core wire to weld the patch in. This is the place to go slow and and not warp the metal. Typically, you must just keep doing spot welds around the patch while giving the metal enough time to cool down to reduce warpage. Keep making the spot wels until you finally have the entire patch welded in.
If you are not an experienced welder, this can be difficult. A bit of instruction from a good welder, along with practice on scrap and you can handle this job if you take your time and make things fit correctly.
