Hi, I don't know if I can help you, but I'll give it a try...
I have an LG phone with Android 6.0.1 and the current version of Chrome.
When I open up my bookmarks, I find a Mobile Bookmark folder that contains a list of websites that I bookmarked. There are no subject folders, just a long list of bookmarks.
Above the Mobile Bookmark folder are the folders I created for various subjects. For example Food, Photography, Cars, Phones, etc. Each of these folders contain a bunch of bookmarks related to the subject. You get the idea.
When I'm viewing a website I want to bookmark, I tap on the 3 dots at the upper right of the screen, then tap on the star. As soon as I tap on the star, a message appears at the screen bottom, indicating what folder the bookmark will be stored in. If I do nothing the bookmark will be stored in the indicated folder. But to the right is the highlighted word EDIT. If I quickly (and I mean within 2 or 3 seconds) tap EDIT, I'm brought to the Edit Bookmark screen that allows me to select which folder I want the bookmark in. I do this by taping on the folder shown, which then shows ALL folders. I can then select the Mobile Bookmark folder or any of the folders I created by taping on the desired folder.
I hope this helps. I found that Google has instructions on bookmarking sites, but nothing about creating and working with folders. I'm still learning about creating bookmark folders and subfolders, mostly by experimentation.