You need a Mac and said Mac needs to have Apple Configurator installed.
In Apple Configurator you import the app you want to install; you need to download the app through iTunes first. Once it's imported into Apple Configurator; if it's a paid app you'll need to import the CSV file with the redeemable codes in. You can download that from the Apple Volume License site. If it's a free app, then it won't prompt you for any codes.
You need two accounts. One to redeem the codes against and another one that you use ONLY to purchase from the Volume Licensing site (sounds like that account is the one you're getting the "This apple id is associated with the volume purchase program for education" message on). I simply have a couple of alias's for this purpose.
When you import a paid app, you'll need to use a different Apple ID to redeem the codes against. I recommend not using your personal one. If there was a chap already doing this, you should already have an account for this purpose.
Certainly the above method is the one I use to manage our iPad's.
Let me know if you need more detail or need me to clarify