Since nearly the beginning of the year, you have been able to get credit on your choice of AA or US FF program when flying either AA or US.
If you have status on one - the you should be crediting the EQM to that airline. I think AA provided enough warning. Pick one airline and put all AA and US flights into that one account.
Why would you in 2014 put some miles in one account and some miles in a different account (unless you are high elite status on both airlines).