We plan to add this directly in wyBuild in the future, but yes, for now you need to stop the service within your own code before it can be updated. You can do this a few ways (including using AutomaticUpdater events), but by far the best way is this:
Stop the services before updating using a batch file
Simply add 2 batch files to your update in the Temporary folder. One batch file will stop the service before an update. The other batch file will stop the service after an update:
Simply check the "Execute file" checkbox to execute the batch files. Read more about Executing files in your update. There are several article online describing how to start and stop services as part of a batch file. Here are a couple that I found in a quick search:
Tell me if this helps.