But if (in the above example) this man had to claim expenses (child fitness, childcare, whatever) for his daughters then how does he do that if he does not enter the daughters on his return?  I am having the same issue and CRA reassessed me and I owe them money now because TurboTax 2013 would not let me enter the credits/expenses without entering all the children.

If you make an agreement to split the children and the deductions, it has to be respected.  You are able to claim all deductions for the boys, you may have to leave the girls' deductions to your wife as agreed.  Ideally, if you pay something for the girls, your ex can claim it.  If she pays something for the boys, you can claim it.  Keep the separation of dependants clean or CRA will step in on it.