How to make online payments without ITIN (for CA)

[lllynx]

Hi, 
I have a somewhat of a silly question to which I cannot find a clear answer.
My wife is still in the process of applying for an ITIN so we will not be able to make the April/18 deadline.
For federal taxes, we are expecting a return so our plan is to just wait until we receive the ITIN number and then file. However, we do owe money for California taxes. I'm currently trying to pay the expected tax amount online following  https://www.ftb.ca.gov/pay/credit-card.html 
Since we are planning to file jointly (after we get her ITIN), I select "Extension payment - Filing Jointly". 
However,  this is requiring me to enter a valid SSN or ITIN (I've tried [removed] and its not working).  My tax preparer (who, at this point, I have very little trust), has told me to just select "Filing individually" to send the payment.  Is this the correct thing to do? (how does FTB know that my wife has paid taxes then? ) . Or should I be mailing cheque and  form 3519 with my wife's ITIN left black? 

[ErnieS0 · Accepted solution]

Your tax preparer is correct. When you finally file a married filing joint return, everything will be combined. You will pay one tax and all your withholding and payments will be added together and subtracted from the tax you owe.

There are no his and her tax payments on a joint return.

You can also send a check.

[lllynx]

Thank you very much for the tips!
I really appreciate your help.