For now I’m happy that things work but I will report back when I find out new interesting things.
I found the “Picture” folder after making it visible in Finder - Preferences - Sidebar.
The technical term would be you added the Pictures folder to the sidebar (which can be seen as list of bookmarks/shortcuts), which makes accessing it easier and faster. The Pictures folder is always visible in the Finder as one of the folders in your Home folder.
The general, default folder structure on OS X starts at the top level of the (boot) drive:
- System
- Library
- Applications
- Users
* YourUserName (your home folder)
- Desktop
- Library
- Documents
- Pictures
- Music
- Movies
- Downloads
- Applications
- Public
- Sites
Of he folders inside your home folder, some have a special purpose, others are just default locations for certain data. The Desktop folder needs no explanation, the Library folder is by default hidden and contains settings files but also a lot of 'internal' data of application, including your actual emails. The Documents folder is where a number of other applications put user-related data (eg, any templates you create in MS Office).
The Pictures, Music, and Movies folders are simply the default folders for the bundled photo (ie, Photos), music (ie, iTunes), and movie (ie, iMovie) applications to store their respective libraries. But you can move the libraries (or create new ones) anywhere you want within your home folder. The Download and Applications folder again are only default locations that can be changed (for files downloaded by web browsers and applications installed only for one user). The Public and Sites folders have special permissions to a allow other users on the computer or even the whole world (for websites 'hosted' inside the Sites folder) to access.
It general is a good idea to not put any data you chose the location for into folders that contain data generated by other applications or the OS itself. This reduces the risk that you modify, move or delete data created by other processes. That includes the Library and Documents folder (though some consider the Documents folder the location for all data you directly create). Most people probably store all their data in custom folders inside the home folder or on the Desktop, though most probably use the Pictures, Music, and Movies folder for those type of files since they are there anyway and cannot be deleted.
Now I drag my images to new folders, that I create in the Picture folder.
In that Picture folder was also the System Photo Library, which I wisely (?) deleted.
It contained the images you had originally imported into Photos. If you have secured those images, you can delete the library. You can at any time create a new library if you wanted to use Photos for something (while you can have multiple Photos libraries, only one can be synched with iCloud, the 'System Photo Library' and I don't know by heart how you assign that status to a given library).
When I insert a SD card, only a small dialog box pops up complaining about that Photos cannot find the System Photo Library. Just quit it. No big annoyance.
If you applied the Terminal command or unchecked that box inside Photos, nothing should be happening anymore when you insert a memory card (unless the lack of a system photo library is triggering this, personally I'd keep a system photo library around, when it's empty it should take up almost no space and it might avoid such dialog boxes, you cannot 'open' Photos without having a library or creating one as part of the launch process, and without Photos, you cannot uncheck that checkbox inside Photos).
I haven’t changed anything in Photo preferences.
But have you unchecked that box in Photos (not sure if you consider it to be part of the preferences)?
Photo might even become one of the many apps I have thrown off the Dock. It gets pretty spacious down there.
PS. removed Photos from Dock. The small pop-up still appears and needs a click on Quit.
Except for the Finder (anchored at the very left) and the Trash (anchored at the very right), you can remove any application from the Dock. The only thing this does is to remove the ability to launch the application via the Dock.