The manifests directory would be located under your environment's path, typically something like
/etc/puppet/environment/feature/manifests. This would be the expected location when you enable directory environments. You can also override that setting with
$default_manifest as described at the same URL.
The files can be placed there automatically with r10k or librarian-puppet, some really awesome tools that will push your puppet code from a version control repository to the environment location dynamically, rather than you having to move files yourself. I would suggest looking into them sooner rather than later (I'm biased toward r10k).