Open iTunes and click on Apps
Click where it says how many updates are available
This takes you to your available updates in the iTunes Store - click on 'Download All Free Updates'
You will need to enter your iTunes account details (the account you download apps for use in Apple Configurator, not your volume purchasing account)
In Apple Configurator, in the Apps tab, click the little plus button as if you were adding an app
In the Select Applications dialog that opens, change the file order to 'Date Modified'
Select the apps downloaded 'Today' and click 'Open'
Apple Configurator will prompt you that you are replacing the app - it will do this for every app you replace (and no, there is no 'Replace All' button!)
For the first app you replace only, you will need to re-enter your Apple ID. Now run Configurator as normal to update all apps in one go!