It sounds like you have two configuration file, each of which has an input, filters, and an output.
If you point path.config at a directory then it will concatenate all of the configuration files in that directory, read events from the inputs and send them to all of the outputs.
I would recommend configuring pipelines.yml, so that you use a different pipeline for each configuration file, or you could tag events on the inputs and use conditionals based on the tags.