One way, is Phantom BOM. It changes the whole structure of your job, so it’s kind of a pain, and you lose visibility of those assemblies, and I’m assuming you want that visibility.
Short of that, You have to complete the last operation for the assembly to be completed and go to the next level. You can use the work queue to do some mass completions, or customize a dashboard, which is what we did.
Here’s a long thread that shows how I was able to make a dashboard in order to mass complete operations. You can tweak your dashboard BAQ and filters to get what you want, and use the start and end activity to complete the operations.