I don't quite understand your question. What exactly do you want to do?
The two mods you want are both in-game mod manager mods (mod.io). You don't need anything from Nexus Mods for that.
Currently there are a problems with mod.io and the checkboxes, the ImpUI mod as well as the unwanted re-downloads if not de-subscribing from the mod.io mods. Is that what you mean?
The Mod Manager is actually only needed if you actually use Nexus Mods, because with Nexus Mods the so-called loading order of the mods plays a role, besides other reasons, and you can and must also set this.
But it can indeed be useful here as a workaround, because you can also use it to deactivate mods. The question is whether mod.io does not reactivate it automatically by re-downloading. Therefore de-subscribing in any case.
Here are some helpful guides for the future:
Mod UsageRemove ModsFull & Clean Uninstall