That sounds like you want to have two independent configurations. If you point path.config to a directory then it will read both configs in a single pipeline, read events from both inputs and send those events to both outputs. You can adjust that using conditionals, but you need those on the filters as well as the outputs.
Misunderstanding this is a very, very common mistake for beginners. (See here and here for examples.)
You can use pipelines.yml to run each configuration is a separate pipeline, which is probably what you want.