When you create a merged patch with FNVEDIT, do you need to merge that patch into the bashed patch as a normal 'merge' file (disable and merge), or is there a special way to handle FNVEDIT merge patches?

No. You can safely merge the MP into Bash's BP. But from my playtesting, the MP causes more CTD's than it prevents. I had consistent 15-20 minute CTD's until I stopped using the Merged Patch. With just the Bashed Patch, I can play for at least an hour without a CTD.