With the Perk you can have two total.. so like 2 zombies or two Storm Atronach, or one of each.
Actually brings up a questions, do Dremora Lords benefit from Atronach perks?
No. Dremora Lords are godawefully powerful without any buffs. I'd say the perk is needed to raise Atronachs up to their bar, outside of the Dremora's lack of ranged combat.
Necromancer is great early, peters off later, and then becomes awesome again at Master. Why? Because you have to find good bodies to raise. This is easy early on, when you have a choice between the average random foe and a familiar. Once you start getting better and better Daedra, then you'll rarely come across an enemy you'll want to raise that'll be equal to, say, a Daedra Lord. I have found some examples of this, however, it is very situational.
Once you get Dead Thrall, though, then things are once again Awesome for the Necromancer. What's better than a powerful NPC raised to your service? One that lasts forever.
There is something else worth trying that I'm probably going to shoot for now that I'm a Conjuration Master -- increasing Smithing and Enchanting. You can load a body's inventory and then raise them, which they'll use to switch out weapons and the like. Finding an awesome body and then loading it up with the best gear you can find seems like an interesting experiment in making a powerful minion.