...Malazan Book of the Fallen...
Here's how I would do it. Now, I'm flying blind here, as there are all kinds of rules and forms of magic I'm unaware of.
Warrens are extra-planar in some way. Some have a physical realm (the Imperial Warren, Meanas) while some (Mokra) apparently have no physical realm.
First, some Runes need to be grouped to form Warrens. For instance, the Rune of Death and Undead both fall under Hood's Warren. Some Runes will be shared by Elder/Lesser Warrens ... the Fire Rune by Telann and Telas, or the overlapping Meanas and Rashan.
And some runes need to be changed. Nothing about the Tiste Liosan or what we've seen of Thyr (or Kurald Thyrllan) indicate "Night Sight," some kind of light effect seems much more applicable. Perhaps something increasing the duration or potency of light spells is more in line with the other Runes.
Each Warren is essentially a group of effects based on the Warren's theme. So I'd make each Warren a skill. Picking up the skill initially requires the sacrifice of POW.
Overall, I'd treat Warrens more like Sorcery than Spirit Magic, to use RQ3 terms.
Next: Magic Points are warren-specific and start at 0, and when you have them saved, drain away at about one per (minute? 5 minutes?). In order to increase magic points you have to open your warren with your skill. Crit Success add a 2D3 Magic Points, Success add 1D3, Failure add 1 MP and a Point of Fatigue (I don't know what that means yet, I'm just brainstorming) and Critical Failure adds 0 MP and 1D3 Fatigue (or closes the warren for D6 minutes).
Each spell-like effect in a Warren is tied to a skill level. So a Master of Thyrr may be able to attempt to make Light at 15% (not guaranteeing success, just making the attempt) but may not be able to create a portal into Thyrr until 60%.
Anyways, those are my "quick thoughts on the matter."