Thanks you both!
I have one more question that isn't necessarily directed towards the topic but still applies to Mod Organizer.
In the "Archives" tab, I'm getting a caution triangle that's telling me "The archive will still be loaded since there is a plugin of the same name but it will not follow the load order!".
If I tick the box, the warning goes away. Is that the correct action choice?
I'm using mods installed by both Mod Organizer and the Steam Workshop.