Can i output the results of a query to different filesystems? For example, query A results go to /tmp/osquery1.results.log and query B results go to /tmp/osquery2.results.log?

As of right now, no. Why are you trying to output the results into different filesystems? Feel free to file an issue with more detail and we can look into if this is a feature we want to add! https://github.com/fleetdm/fleet/issues/new?assignees=&labels=idea&template=feature-request.md&title=