There are multiple ways to do that.
You can open the folder in the bookmarks bar and select the option to add a bookmark there, this will bookmark the current page in that folder.
You can drag and drop the bookmarks into the folders you want.
In the latest Opera testing builds (Opera 20) I'm able to drag a tab (or grab that little symbol in the left side of the address field) and drop directly into the folder you want in the bookmarks bar.