I don't get the whole Zod story line. Didnt he possess Lex and Clark banished him to the Phantom Zone? How did he get out and where did this army come from?
They are actually two distinct beings that diverged from a single one many years ago. Zod did not go bad, betray the ruling Science Council of Krypton and get sentenced to the Phantom Zone for eternity until he was a General. This Zod is Major Zod (a couple of ranks below General). Or at least this Zod was grown from a blood sample and stored memories of Major Zod contained within the Orb that Tess unleashed at the end of last season. The fate of General Zod remains the same, as the clone Major Zod has no bearing on what happened to the General. The Orb was apparently a genetic back-up file of Krypton's elite, designed to keep the race alive should Jor-El (the Orb's creator) fail to save his people from Krypton's destruction.
What I think is confusing you is that the clones don't yet realize they are clones. They assume they are the originals who were somehow transported to Earth.
And there is a clone of Jor-El running around in Turkey now as well (and likely the only one of the new Kryptonians who has a real idea of what is going on, since he has the memories of why the Orb was made and why blood samples and memories were duplicated in it). A duplicate made from before he and Lara had a son most likely. It is going to be interesting to see him meet a grown son he never knew he had. And I wager he gets a trip to the Fortress, a download of the memories that his older AI self in the Fortress has, and his full powers unleashed. And I like their choice for the actor to play him, as long as they dye his hair black. I won't say who it is. Spoilers are out there if you want them.