In Oblivion, the Mages Guild, or at least Raminus Polus, doesn't seem to have any idea what black soul gems do, or how they are made. One of the quests is doing research on the subject and he says:
What little we know makes no sense in a larger context. For example, why was http://uesp.net/wiki/Oblivion:Falcar -- who we know now to be part of this cult of Necromancers -- in possession of http://uesp.net/wiki/Oblivion:Black_Soul_Gem? The Arch-Mage has other reports of these gems being associated with Necromancers, but we do not know why. We don't even know what they do. We have overlooked these questions because we are so focused on rooting out the Necromancers as quickly as possible.
It seems rather unlikely to me that a Guild that has had necromancers in it for years, in an Empire where necromancy is legal, wouldn't know what black soul gems do. Unless the necromancers just kept their research secret?
Then Dawnguard comes along, and we see that Serana and Valerica are necromancers. Valerica (probably?) predates Mannimarco, but is definitely a skilled necromancer, and has been doing research for years- into the Soul Cairn. She describes how undead summoned from the Soul Cairn are much more powerful than ones raised by a necromancer, and, if I recall correctly, refers to this sort of necromancy as a lost art. And we also see that black soul gems clearly can be created independently of Mannimarco, because they can be found and created in the Soul Cairn. Are there any other ways to make them?
Can all of this be fit together somehow?
Maybe once Mannimarco ascended to godhood, necromancers began worshiping him and using him as a source of power rather than having to make much riskier deals with the Ideal Masters?
I have not played as much of Morrowind as I should, so I'm not sure how that might fit in here either, any thoughts?