Be aware that my JSGME doesn't tell the whole story. I have many mods that I tested with JSGME and then installed permanently, so they aren't represented in the screenshot.
One of the things you pick up after awhile is the ability to see the 'override' warning and recognise whether it's something you care about or not. For instance, when I activated Rick's Recognition Manual, it warned me that another mod had already changed all the Sil.tga files. Changing those was what I wanted the mod for in the first place, so I knew right away it didn't matter.