So is season two just like this or did they let the past be changed which would of changed the characters future?
It's utterly confusing.
They've already basically implied that the two times are separate as they killed one of the time traveler's ancestors without him popping out of existence. So changing the past obviously can't have any impact on the future.
The confusion comes from everything else that happens.
Older Alec keeps giving these creepy knowing smiles when he sees Kiera, suggesting that he remembers the experiences in his past. This is all but confirmed if what we reveal about Alec's father turns out to be true in the second season; clearly those events occurred and he had to have been responsible for them, else they couldn't have occurred at all.
But he also seems to have orchestrated the entire scheme in order to change the future he created by influencing his past self to make wiser choices. If that's the case, and the plan worked, then... well, it just doesn't make much sense as he wouldn't have needed to try to influence the past. Unless its a goofy predestination paradox sort of deal.
BUT then that all gets in the way of what we learned in the first point above; that changes to the past don't have any apparent impact on the future. Else Kellog wouldn't be around.
It's even more confusing because we've also been shown that people arrived at different times, meaning that any impact any of them had in the past should/would have influenced the future that the others arrived from. Which they apparently didn't.
So I don't know what to make of any of it. It can't be separate timelines because of Alec's parentage. It can't be the same timeline because of Kellog's existence. So there must be another option that I'm just oblivious to.