You do not need to reference pipelines.yml in logstash.yml. If you do not pass it any config files (e.g. -f) then logstash looks in path.settings for pipelines.yml
To the second part, you can pass either a single file or a regexp to a pipeline. Thus you might have
- pipeline.id: foo
path.config: "/etc/logstash/conf.misc/DoFoo.conf"
# or
- pipeline.id: bar
path.config: "/etc/logstash/conf.bar/*.conf"