There are two different things here, and you can definitely use both Filestore and Datastore at the same time:
To automatically add CSV files to the datastore whenever a dataset is created, you can use the DataPusher extension. This is a standalone service that runs on the server and uploads new files to the DataStore, regardless of if they were uploaded (via the Filestore) or are hosted somewhere else. (note that the old datastorer (with an extra r) is deprecated and no longer used).
To fix the errors you are getting when setting up the Filestore, check this answer with tips on what to check: Error when trying to upload a file to CKAN: "Failed to get credentials for storage upload. Upload cannot proceed"