Best practices for syncing music on iPhone 6?

Absolutely, a playlist (or group of playlists) can be synchronized to your iPhone to define what you want on it. If you auto-sync to the selected playlist(s), any rating changes (and play history) that you make on your iPhone transfer back to iTunes on your next sync. Since you're in control of the playlists in iTunes, you can manage the size and content of what's on your iPhone.

In my case my library greatly exceeds the capacity of my iPhone, so I have several smart and regular playlists that help "shape" what gets loaded to my device. Smart playlists have the advantage of automatically choosing songs from your library based on criteria that you define (ratings, play count, play date, etc.) and they can be set such that once a song plays, it will be removed and replaced on your next sync to iTunes. I use regular playlists for new material, or songs/albums that I always want on my iPhone.

Get creative, it's a lot of fun and a great way to rotate through your library even with a limited capacity device.

That I'm not sure about ... I've heard that manual management allows syncing of information, and I've heard that it doesn't. Perhaps it did at one time but no longer does so, which may explain why something seems to have changed for you.

IMO, there's little reason to do manual management, as you can accomplish the exact same thing with a little mindset change. Instead of manually managing your device, you manually manage a playlist (or group of playlists). There really is little difference, except that if you manage playlists then you get the benefits of syncing, always.

There is an in-between option that is not talked about much, and most don't know. You can auto-sync and still manually drag and drop content to your device. Updates to the manually added items may not sync back to your library, but you can auto-sync a group of playlists and manually add whatever else you want. I don't know why one would want to do this, but it is possible.

LOL! Trying to keep up with iTunes changes and features (and bugs) seems to be a full-time job these days!