Simple as that, just get some of that sheet foam and cut it out to fit the pouch, you may need a few layers depending on the thickness. I don't know for sure, but I believe they had a battery in at least one of the hip pouches for the chest lights, they probably filled the rest with sheet foam or cotton batting (I find the sheets hold the square shape better).
I did'ent like how the foam looked in mine (looked too block-like), so I used polyester batting like you would find in pillows and I was VERY happy with that. You can get it at most any fabric store super cheap.
I plan to pad mine the same way I pad my bikerscout. I went and bought some cheap tupperware. I cut one end open. I then shove the tupperware into the pouch. It gives the pouch shape and it is still usable. You can find the cheap tupperware at any Dollar store, Walmart or K-Mart type store for around $2. Try it it works great.
My side pouches I used old mayionase containers. Can't remeber the brand but the shape of the container is almost perfect and they are still useable as pockets. My thigh pouches I am using foam at the moment but I am looking for something else as the foam holds to much heat. I start to have sweat run down my leg some times.... might try a open celled foam or the batting.