What kind of apps? App Store apps? 3rd party apps such as Audacity, Adobe, Chrome, etc..?
I know there's a setting for the App Store apps if they are purchased through your VPP (Apple Business Manager or Apple School Manager now).
If they are 3rd party apps:
I use autopkg to update Adobe Flash, Adobe Reader, Google Chrome, Mozilla Firefox, Skype, and VLC Media Player; I have scripts to download them and rename them according to my naming schemes. For Audacity and Jing, I download them manually and repackage them from DMGs to PKGs using scripts. Once the PKGs are generated, all I have to do is upload them to Jamf Pro and resync my distribution points and update my policies and patch policies. Definitely faster than having to download everything manually.
Here are the scripts I use: https://github.com/redninja2/jamf-scripts
