I'm pretty certain you can't. As soon as you import the app into Configurator it will ask for the codes, or else it won't allow it to be sent to any devices. If you've only bought one copy of each app then that's not a huge problem (both costing £2.99 each).
However, if you've already bought 15 copies of iMovie and Garageband and they're installed on the iPads, make sure you go to the Configurator preferences and uncheck the option that says "Remove apps and profiles Configurator did not install" before you connect the iPads. I've not tried this myself as I have used Configurator to install everything but in theory it should work.

