Quick question- I've Lucien following me right now and he's been pretty solid for me. I also use Dremora Lords and Atronachs off and on. In the past if I've cast one of those, Lucien disappears. I just reached 100 for conjuration and have all the atronach and necromancy perks, but not the entire Conjuration tree.

Now that I have obtained Twin Souls, is there any way I can keep Lucien and also summon another zombie/thrall/dremora/atronach?

No. Lucien is not a normal summons. He's a power that can only be used once a day.

http://www.uesp.net/wiki/Skyrim:Spectral_Assassin