The premise of the Unificators is that they use souls as fuel. The Cult acquires souls from its fanatics, some of which are psychics. Those specific characters are trained as Dominators to control the masses more effectively and thus strengthen the Cult. Soul Cubes are specially designed to hold and process the souls that fanatics willingly, or 'willingly', part with.
I personally wanted to play around with the idea of a third pseudo-resource, and so the Soul Cube embodied that role. To make them usable across the entire Unificator army, there are 3 mechanics that they use: Docking, Soul Transferal and Piloting.
With Docking, the Soul Cube can dock onto buildings in the same way Acolytes dock onto Haunted Gold Mines. This process is completely custom-made and can be controlled however I want to. In the case of the Spirit Well, Docking Soul Cubes onto it will allow it to regenerate mana faster. This is necessary sometimes because Unificator buildings need mana to not lose health and ultimately expire - but they also use mana as a shield. A Unificator building that gets damaged will progressively lose damage resistance - so having a Spirit Well nearby transfer large amounts of mana back into it help maintain it's damage reduction.
Soul Transferal is your basic method of unit production. Frabricators and Advanced Fabricators will automatically generate Empty Husks for you free of charge every 25 seconds, and you must sacrifice Soul Cubes on those Empty Husks to upgrade them to various forms. Once an Empty Husk is fed 2 Cubes, it morphs into it's basic form. An additional Cube morphs it into it's advanced form. Ordering a morphed Husk will charge you the relevant amount of lumber and will activate the Husk.
The Spire is a strong support unit that is mostly a proxy for Cubes. Cubes can load up into the Spire, which the Soul Projector can then use as fuel for its spells. The Soul Projector is also able to Soul Transfer from a distance, which makes them useful for when you acquire the Immortality Protocol upgrade in late game.
Piloting, for Soul Cubes specifically, serves two roles: one is to allow the Cubes to empower Bane Chariots (siege units) and Annihilators (strong crowd control) to make them stronger, and the other is to allow the Cubes to travel alongside your army safely so that you can use them as fuel to resurrect some fallen Husks. This fallen Husk mechanic is called the Immortality Protocol, and it allows you to revive Husks by sacrificing your Soul Cubes. The number of Soul Cubes required is the same amount it took to create them in the first place, but you are not charged any lumber, which make this a more cost-effective way of maintaining an army. It also follows the Undead theme as being an army that never dies.
Piloting is also available to the Dominators and Mechaweavers, the caster units of the Unificators. As we wanted to keep the mechanics similar to those already introduced (aka Soul Transferal) we thought having existing units assume new roles would make for an interesting take, and so the casters were given the ability to Pilot Bane Chariots and Annihilators. We wanted to make the Piloting mutually exclusive, aka, if you allow the Dominator to Pilot the Chariot, the Mechaweaver would not be able to. Without this restriction, the total number of units goes up to 14, so limiting the Piloting would have put the number down nicely to 12.
As far as the Nerubians are concerned, the same thing happens to them as it happened in vanilla wc3, but the difference here is that we made the Nerubians into mechanics, given the Unificator's focus on mechanical units. Vanilla Nerubians did have a penchant for intellectual works, after all, so it wasn't too far a stretch to place them into the Mechaweaver role.
A final bit of note, for the sake of balance, the Husks (Battle Husks, Scourge Husks, Disruptor Husks and Predator Husks) are all Organic. We explain it away in the lore by saying they are a mixture of machine and Undead flesh. The flesh part makes them vulnerable to magic. The same applies to the C.R.P.T. hero, a bio-mechanical tank. That being said, Husks that have not yet been activated are immune to magic, again for balance reasons, but also because they don't have 'souls' inside of them yet.