I am not familiar with Malazan, so you might have to explain a little bit about what the setting is to me.
Now, if I were building a system for using Spell Bases as the core of a magical system (and I have given this some thought, and in fact I think I may have mentioned it before), there are a couple of ways of going about this, but this would be my initial take on it, based upon what is in your first post.
You could create a table, that grants bonuses or minuses to specific Bases (+2 to -2; sum of all modifiers = 0), and then give each Warren (I would guess that this is the equivalent to School) certain Spell Bases, and the rest would be more along the UnWarrened. You would have 1 skill for Warren bases, and 1 for those not part of the Warren. (the skill bonuses would be modified at the time of casting by the Base Modifiers.
You would then allow the characters to start with 3 Spell Bases (Warren Bases only), every additional Warren Base costs 3 points (one time cost) and non-Warren Bases cost 5 points (one time costs). When building a spell's TN, I would perhaps lower the base of the TN from 12 to 10 for those Bases belonging to the Warren (but not the others). I would also allow the Warren Bases to use the Codified costs, while the non-Warren Bases use the Improv column.
This allows for more powerful spells being accessible to those within a given Warren, but not overly powerful