I am using Behaviors to automatically add a user to a custom field from another custom field in a workflow transition. The issue that I am having is that it will pre-populate the issue (correct) but if I want to modify the value after that, it does not let me and just overwrites it with the previous value.
Is there a configuration that I can make to allow me to modify the value?
You need to put that behaviour not on the field that's being prepopulated, but on the field that it's getting it's value from. By default it fires everytime it's edited, which explains why it gets overwritten.
If you want to only populate it if it's empty you have to handle that in code, eg:
if (! targetField) { copy from source field }
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