Rick
The res system is treating you as one PNR - thats why Skywards is trying to deduct from the one single account.
In order for you to deduct from each account, you will need to see if EK can split the res into 2 single PNR's, thereby allowing you to deduct miles from each account.
I know you can do this with other carriers such as UA, (but not without some effort and an agent who knows what they are doing)
You're going to have to call them I'm afraid. And persist if the first agent doesnt or cant do it. Call again - the old FT mantra.
Cheers
SIMON