I'm not really clear on the question. Yes, you can use wyUpdate to update multiple programs. Yes, you can automate it. This is covered in the marketing materials, and more in-depth in the help articles: https://wyday.com/wybuild/help/walkthrough.php
I am part of a Search and Rescue group whereby we have several programs in various directories, specific to SAR, that are updated every so often. If we have a task started each day that fires off wyBuild/wyUpdate can it check for updates on a server for the multiple programs and operate on those needing an update? Is the program changed for updating different versions or just the information contained in the xml file?
Hopefully the intent of the above questions are clear.