I also use bamboo skewers - today I tried putting them in flat end first so that I can use the pointed end to stick into my foam.
I put them in just out of the oven while they are still on the pan. It's easy to push the stick into the warm cookie and it sort of bakes onto the stick while they cool down. I do have to think about where I'm putting the cookies on the sheet when I bake them, but it's very quick and easy.
One thing I learned the hard way...when putting the cookies into your container, be sure to hold only the stick part...I had a ladybug slide all the way down the stick as I tried to insert her in foam by pushing from the top...oops! I always bake and extra of each shape "just in case"