Having read the Sheol Saga and both Nyytian Trilogy books, my guess is that they take place in the same universe. The reason being that both feature brain implants that give the user a HUD, extend their lifespan, and are accessed by a flap of artificial skin behind the ear. That seems to be the only concrete tether between the two stories. However, it's such a specific combination of attributes that I think they have to be referring to the same technology, and so the two stories are likely in the same universe. But, I can't figure out which one happens first.
If you haven't read it, the Nyytian Trilogy takes place in a future where humanity had advanced to a point where they could put lots of space stations in orbit. Something causes all of the stations to fall, which sends earth back to the stone age. The Nyytian Trilogy takes place when humanity has advanced back to something approximating the industrial revolution. There are aliens in the story, and they are ostensibly the reason that the stations fell. Notably, these aliens do not appear to be any of the races described in the Sheol Saga. Regardless, first contact has been made, which is the part that makes the two series difficult to place on a timeline.
Because the Sheol Saga features a humanity that has advanced far beyond any era described in the Nyytian Trilogy, I think it is easy to assume that the Sheol Saga happens second, and that the timeline goes something like this:
All of actual human history through the present day
Humanity puts space stations in orbit
Alien attack
Stone age through industrial age
Nyytian Trilogy
Advance back to space faring age
Sheol Saga
BUT, the Sheol Saga describes how humans are something of a galactic commodity and all of the other races put a lot of money and effort into keeping us alive. Even going so far as to make earth something of a wildlife preserve for us until we could fend for ourselves. So, I think if earth had been attacked while it was still a preserve, that the other races would have protected us/their investment. Yet we know that didn't happen. Earth was attacked and it doesn't seem like anyone tried to intervene. And if memory serves, the Sheol Saga doesn't mention anything about earth having been devastated in the past. To me, that suggests that the Sheol Saga actually happens first, and the alien attack happens after earth is no longer considered a preserve. The timeline then goes something like this:
Sheol Saga
Alien Attack
Stone age through industrial age
Nyytian Trilogy
I'm not actually sure which timeline makes more sense to me yet. There's circumstantial evidence to support either one. Option 3, of course, is that the two stories are not related and Mr Comer/Gaumer just really likes the idea of that brain-computer interface and wanted to use it again.
Dig it. :)