What's best practice in terms of handling Gift Aid within CiviCRM
You are correct - the Veda extension is for submitting the Gift Aid application to HMRC and the Compucorp one does the rest. It's a shame this isn't better documented. Be careful of the version of the Compucorp one though, as I don't believe the one of the Civi extensions page works with 4.6 - get a working version from Git here