I stuck a jerkbait into the knee of my waders, so I bought a patch kit from Wal-Mart, and went heavy on the glue that came with it. Then, I applied a lot of heavy duty glue. Let it cure for a few days, then I took some waterproofing spray and coated my entire waders. Fixed them right up.
Since your holes are along a seem, I would patch them up good, and hit them with some waterproofing spray. Make sure you let them cure for a few days before wearing them.