Right. The links are automatically set so you can keep the bottom clips together with the top clips. The work flow would be to edit the bottom clips and then add and edit the top clips. Or, you can create a project with just the top line clips in it, edit it, export it out, and then import it into a project that has only the bottom line clips in it. Overlay it onto the bottom line clips and then edit the bottom line clips. See the third option below.
Make a duplicate of your project first so that you preserve your original. You can then experiment with the duplicate project.
Working with the duplicate project, try selecting the top clips as a group, and then do an Edit/Cut. Now edit your bottom clips and, when finished, do an Edit/Paste to add back the top clips.
Alternatively, you can slide the top clips to a location elsewhere in the timeline. Then edit the bottom clips and slide your top clips back into place.
Here's another way, and this may be the easiest. In your duplicate project, Edit/Cut the edited top timeline clips and Edit/Paste them into the bottom timeline. Then delete the bottom line clips that you previously had. Share out the project with just the previously edited top line videos in it. Then import the shared out movie into a project that just has your bottom line clips in it. The shared out movie will come in as one clip with all of the clips locked in place together. Overlay your shared out movie, as one long clip, above the bottom line clips. Then you can edit the bottom line clips without disturbing the sync of the top line clips.
Looks more confusing when trying to describe it versus doing it. Experiment a little and see if you can get it to work the way you want.
--Rich