Sorry think I've sorted it!
@betty02 Could you let me know how you packaged Keynote 6.6 up and deployed it. How did you get the update package?
Much appreciated!
@Omar The way I did it was an easy way, installed it on my Mac, opened up Composer and dragged the App in, make sure I deleted the MAS receipt too, and then built it as a PKG! I was advised by some this was the best way and easiest way, then advised by others it wasn't. It has worked great here for us and has been fine! Hope this helps!
There are ways to get an installer package for Keynote directly from the Mac App Store. I have a post that discusses one method available here:
https://derflounder.wordpress.com/2015/11/19/downloading-installer-packages-from-the-mac-app-store-with-appstoreextract/
Thanks @betty02 and @rtrouton , I will give both methods a go.
I distribute these following rtroutons method. Just make sure that you understand that the update will still present itself to the user via the Mac App Store as it doesn't have a receipt pointing to that users AppleID (Or any for that matter). Its a bit "cleaner" than using composer but it's the same idea, essentially, i.e. creating a receipt-less app.
There is always VPP too, but I've found that to be difficult to manage with a student owned BYOD program. You'd think a free app would be simpler to deal with ;-)
That said, Keynote is a super easy one. Garageband and it's extras are a little more interesting.

I use the Terminal to capture the package as the App Store is downloading it. Become root with:
sudo su
Then use the find command to look for a file named star dot pkg under /var/folders/
Then cp -Rpv the file from source to destination using copy and paste for the long pathname.
Timing is important. You don't want to copy the pkg before the App store has finished downloading it, but you must complete the copy before the App store has finished installing it or it will delete the file before you can get it. Example screen shot above.
Of course now that this is posted publicly we can expect Apple to change something so this process breaks. ;)
Another option is to open Console while it's being downloaded/installed, you'll see the temp path.
We have the App Store blocked and removed/hidden so thankfully they don't see it showing as an update required! @endor-moon I like that way! But if you miss it, your buggered haha!