I have been trying to learn this system and it is not all that bad, actually rather unique in many ways.
Apple's approach is centered on using the Local Computer Apps for each task and then iCloud being an extension of that. iCloud keeps a copy on iCloud.com for web access and also syncs to your other machines.
So in some ways it is more of a sync client.
Google's approach is to do all your work in the cloud with no great need for local apps.
So as far as pictures I would make sure to learn the intricacies of the Photos App as best you can.
To have a 360 degree upload to iCloud you need to...
-Add all your Photos to the Photos App.
-Add all your Music to iTunes and Subscribe to Apple Music.
-Keep all your documents in the Desktop or Documents Folder or the main iCloud Folder or have opened them with Pages Keynote or Numbers.
-Enable iCloud storage for all these services.
It took me a little to get on to all this as I was used to dumping all my files in a big cloud folder on my computer somewhere and it all being uploaded to the cloud by a sync client.
The optimize storage feature in Sierra is a new way to keep you Desktop and Documents in sync.
And you still have the main iCloud Folder to create your own cloud file system in.
As for photos your photos are stored in a database and can be exported as original quantity whenever you want. The same is true for iTunes.
Maybe the Photos App should automatically import the contents of the Photos Folder.