The three types are charged differently.
The neutral one is fairly simple- put in any accepted Rustbound Magic item or a temporal gear in order to charge it.
The Dark Nexus can only be charged by bringing creatures other than players next to it to drain their life energy.
And a Light Nexus recharges and gains essence overtime, but only when exposed to sunlight(Meaning it only charges during the day without a roof).
I have had a few friends that tried to charge a Light Nexus indoors, and I had to show them the right way because they complained how the Light Nexus wasn't charging. It tells you in the Guidebook you can craft with a fiber and rusty dust how each nexus works and how to upgrade them- along with any rituals and world magic stuff.