BlackRoses, I honestly don't think it matters what we think
We're not the ones who will have to raise them... What do YOU think about having other kids with your secondary?
In terms of it being with the secondary and not primary, I think this is the exact place where those kinds of labels stop being useful. You've been with her for 6 years, you both presumably love her (going by the usage "we've been with her" and not "I've been with her"), she's probably a part of your family, and you're now considering making babies together and raising your family together.
At what point does she get to become an equal partner in your family? Or will she never be allowed that privilege simply because she hasn't put in as much time as your wife?