Two processes is normal - TS v3 uses Sphinx's threaded workers (so, you're seeing the master process and at least one child).
As for the ts:stop issue - I presume this is via Capistrano? It's probably because the configuration file doesn't exist for the current deployed release. You should probably change the file location (using the configuration_file setting) to somewhere in the shared directory.
This is covered in the deployment documentation (but was only added about a month ago).
As for the yml settings - you can remove searchd_file_path
, as it's been replaced by indices_location
in TS v3, and config_file
should be configuration_file
.