Some clarity, Monkhound:
Kellhus is shown to have seen sorcery as early as TDTCB. When he's running from the Nonman he comes to a place that is marked, and he mentions something about it.
Kellhus is also super smart, he was just able to figure out that he sees things in a way that some people do not - the Onta. It has a distinct appearance, see: Achamian's flashback to when his 'inner sight' first opens.
Seeing the Onta, the fabric of creation, is separate from being Marked. Those of the Few see the Onta, which includes the mark of sorcery, but its also independent from that. Everything looks different to those who can See.
As discussed above, the Mark is something comes about from the practice of sorcery, and can be on a sorcerer (often described as a Mark, a Bruise, or more formally 'The Blood of the Onta'), or it can be on objects that sorcery has been used on. There are several instances of objects or whole swaths of battle fields being 'marked' after battles.
The Judging Eye is somehow tied to pregnancy, but also separate. I believe Mimara herself says that she has had this 'other sight' for as long as she can remember. This sight, btw, is entirely separate from seeing the Onta as described above. Onta is the fabric of creation, the Judging Eye sees what appears to be some kind of morality, good vs. evil, etc.