Can you please clarify what you mean by "529C"? I've never heard of a 529 plan or account referred to as a 529c -- maybe it's something new or rare, or I've just had my head stuck in the sand.
Do you mean does it matter where the funds come from that establish a new 529 account or add to an already existing 529 account? No, it does not matter.
A 529 account can only have one beneficiary, so if you have two boys and you want a 529 account for each of them, you will need to set up at least two accounts.
I don't know enough about New York state tax law to answer your main question, but I would think that one obstacle might be whether or not the New York tax deduction for a 529 contribution is available for non-residents who happen to have a New York income tax liability based on New York state source income, as is your case. I would start with that inquiry.