Hey @noobman2logstash,
You can run multiple instances of Filebeat in the same host. You can use the same installation and binaries, but they need to use different data paths. You can configure the data path with path.data. This data path can be configured as a runtime flag, so you could do this:
.\filebeat.exe -c filebeat.yml --path.data somepath
.\filebeat.exe -c filebeat2.yml --path.data someotherpath