I haven't used Opera for ages so here's what I did to get it all working properly.
First I exported my bookmarks from Chrome. Next I started Opera on my work PC and logged in to Opera Link. I then cleared all my old bookmarks.
Next I imported my Chrome bookmarks and sorted them into the correct order. I also setup the Personal Bar and setup Speed Dial as a 3x3 grid with my 9 favourite pages. Finally I copied all my bookmark folders to the Opera Mini folder within my Opera Bookmarks.
I then went to Opera Mini and signed in to Link. It updated the 3x3 speed dial to mirror the desktop speed dial and also synbched the bookmarks from the Opera Mini folder in the desktop bookmarks. I think this is the main bit you're missing.