Since you are asking two unrelated questions, I will split my answer into two parts:
Did Vaatu create the Southern and Northern portals?
We don't know: Both portals are treated as something existing from immemorial times, from before the Avatar Era.
Since Vaatu claims to have been the first one to transit between the two worlds, we could consider logical that he created them, but in this case, why create two, when only one was necessary? The portals may be natural weak-points Vaatu only discovered (note he does not boast about creating the portals themselves), or Raava could just as well have created them to introduce more spirits into the physical world, since she considered them less chaotic than humans.
Why did not Raava or Vaatu lose long before humans come into existence?
Raava or Vaatu can never be destroyed for good, be it during an Harmonic Convergence or not, as explained by Raava in Beginnings, Part two:
He cannot destroy light any more than I can destroy darkness. One cannot exist without the other. Even if I defeat Vaatu in this encounter, darkness will grow inside me until he emerges again. The same will hold true if Vaatu defeats me.
However, Vaatu can be freed during Harmonic Convergence, thanks to the energies liberated from the two portals breaking his jail:
That's why Harmonic Convergence is important, not because if would permit any of them to destroy the other definitely, since the victim will always reform by the next one