Here is your plan of action ... efile both at the same time when they are both ready to file since you do not need to pay the feds when you file ... you have until 4/18/17 to make the payment which is more than enough time to get the CA refund in hand (efiling will be faster than a paper return).
In the FILE tab simply choose to mail in a check for the federal balance due then you can either mail a check with the voucher that will print out OR pay online at the IRS web site here: https://www.irs.gov/payments