So, I'm sure different folks do different things, but I use Munki's built in option for custom conditions to control whether licensed applications can be installed or not.
Essentially, I have a folder of what I call "Software Markers" that is available to our Support desk. This is just a term I made up for them to understand - the files are just tiny script files that set custom conditions that Munki can read and evaluate against.
As an example, in the "Software Markers" folder there is a file called "adobecc.sh", which contains the following script (pretty much straight form the Munki documentation):
#!/bin/sh
managedinstalldir="$(defaults read /Library/Preferences/ManagedInstalls ManagedInstallDir)"
plist_loc="$managedinstalldir/ConditionalItems"
defaults write "$plist_loc" "adobecc" -bool Yes
plutil -convert xml1 "$plist_loc".plist
exit 0
When an authorized, licensed user need Adobe Creative Cloud installed the Support Tech send this file to the machine in question (always copied to /user/local/munki/conditions, where these things "live").
The package in the manifest is set with a condition of adobecc = YES.
Now, the next time the user runs MSU (or MSC) munki will check if the "adobecc" condition is true (which it will be), and the software will be offered up to the user along with anything else that is appropriate.
The user can then still self-service install the app along with any of the non-licensed apps, in the fashion they are already used to. If they are authorized it is presented to them, if they are not, they see nothing.
The for us, then, is essentially: The user calls support and requests the software; Support confirms the user is eligible; The Support Tech sends the marker file to the user's machine; They then inform the user that they can now launch MSU (MSC) and install the application at their convenience.
It really sounds more complicated than it is, once you do it. :)