Default bioware AI can't use scripted spellbooks. That's why probably all 'new' spellbook classes (psionics, blade magic etc.) are not the best choice for cohorts.
Cohorts made with standard bioware classes can use spells, though you can't choose spells prepared on different levels. You do however select the spells that the character can cast - simply before advancing to final level during cohort registration process, modify characters spellbook. The cohort will cast spells you memorized during that level. In theory, you could create several versions of the same cohort with different spells.
