Create the character you want to be an undead boss (like, for example, dwarf fighter 3/rogue 3).
Apply the undead template you want it to be, to it (Wight, Zombie, Skeleton, Dread Warrior... some undead, such as mummies or mohrgs, don't work so well as templates).
Assume it has had the Awaken Undead spell cast on it, or it is an alternate version that is not Mindless (juju zombie, dread warrior instead of skeleton etc), and so therefore ignore any parts of the template that try to change your character's int to zero or make it mindless or anything else like that.
Voila. After you make the changes the template says to make (getting rid of Con score, giving undead type/immunities, giving any modifiers to attributes or abilities/skills (skeleton template's +4 untyped modifier to initiative, for example)), you should have the character ready to play.
However. I would suggest giving these minibosses either the Unholy Toughness ability (MMIV) (lets them use cha mod instead of con mod to get bonus hp - normally you lose all bonus hp when you lose your con score cause of undead and all your HD get turned to d12s) or have them be created by a Dread Necromancer with either the corpse-crafter feat or a desecrate effect - giving them +4 HP per HD.
As written, characters with undead templates don't make good minibosses cause due to no con score they go down too fast, especially the fighter types.
