I have three young sons, so jeans whith wholes are well known around here. It's a known fact that fitting those tiny little pants under the sewing machine is almost impossible. But if you use your darning foot it can be as easy as pie.
You need some vliesofix, a darning foot and some sturdy fabric. I use denim.
Iron vliesofix unto the denim, and pull the paper off.
Cut the denim into suitable pieces. I usually make a whole stack when I'm at it.
Zigzag the patches. I use my serger because it's fast and the seam looks nice.
Iron the patches to the pants.
Use the darning foot and set your machine as if you were free motion quilting.
Sew around the patch. I also like to make a few seams across to make sure it will stay put.