The best way, in my opinion, to set up a massive undead army is through a pyramid scheme. You control X number of undead that, themselves, can summon and control undead which can, in turn, create undead that can do the same until the lowest level controllers are controlling all of the 'mook' undead.
This could also provide some strategy or role playing sessions as your players try to neutralize mid- to upper-level controllers to break some of the control the master NPC has over some portion of his army.