I presume that you exported your Vivaldi bookmarks on your old Mac to an HTML file.
With a new, fresh installation, your default Bookmarks should consist of a "Speed Dial" folder and a "Bookmarks" folder.
When you copy that HTML file to your new Mac and, using the Bookmarks Manager, import the Bookmarks HTML File, it should create an "Import" directory consisting of Bookmarks and Trash. That Bookmarks folder should contain the entire hierarchy of bookmarks that were shown on the Bookmarks menu on the macOS menu bar of your old Mac. You can select all of the bookmarks and folders that you want to copy and drag them to a point "above" the bookmark folders that are provided in the default install. When you have things the way that you want, you can delete the Import folder.
If all that proves to be too difficult, you can also try going into the Bookmarks Manager and delete ALL of the bookmark folders, including the Import folders. Now, when importing the exported bookmark HTML file to an empty bookmark tree, it will no longer create a Import folder. Instead, it should restore the bookmarks exactly as they were in Vivaldi on your old Mac.
It sounds like you also used the Bookmarks Bar. By default, it will display the entire bookmark tree. If you want the Bookmark Bar to show subfolders of a "favorite" folder, go in Preferences... , go to the Bookmarks section, and select "favorite" from the drop-down under Select Bookmark Bar Folder.
I hope this helps and hope this all makes sense.