All photos not syncing with iCloud photos

• Then I made the folder with all the stored pictures as the system folder with .photoslibrary file

What do you mean by this? To sync with an iCloud Photo Library you need to import the images into Photos, and the library has to be a: managed and b: on a disk formatted Mac OS X Extended, Journaled or apfs.

As Yer_Man says, you would need to do this:

Make a New System Library connected to iCloud… - Apple Community

to make a new Photos Library on the external drive. It will fill with what is already in your iCloud Photos at iCloud.com. And then you can use Photos' File>Import to import the new pictures.

If your picture files are in separate folders, then In the Import dialog, you can choose "Keep "Folder Organization"

to keep pictures in Albums made from the Finder folders.