How to file CA State return while applying for ITIN for my spouse.

You will want to file an extension for your state until you receive your ITIN. This is because the application for your ITIN is a federal filing. Most state will not process your return without either a SSN or an ITIN. (However some states will accept state filings with W-7 attachments. You will need to contact your state's Department of Revenue and ask if your state will accept a state tax return with a Form W-7 attached).  
When the IRS assigns you an ITIN, update your returns (both federal and state) in TurboTax with this new information and then you should be able to e-file your state return. 
Because many states give an automatic extension when you file the federal extension Form 4868, just file a federal extension even if you don't think you will need it for your federal tax return.  But check with your state's Department of Revenue to make sure that your state doesn't have a separate state extension filing.

https://ttlc.intuit.com/replies/3302452

It's confusing. I have paper filed my federal taxes as I needed ITIN for my son. Now I got ITIN, can i go ahead and efile CA state taxes? Somewhere in turbotax, I have read that, you won't be able to e-file your state if your federal return was, or will be, paper-filed. As I understand, since I have paper filed my federal taxes, I must need to paper file your state taxes as well. Is that correct?

That is correct.. I had to paper file our state return for the same reason though I had paid turbo tax for efile.

Thank you.

This is what I understood after talking to CA tax department -

For CA State Tax returns you just need to mention as "Applied For" in the SSN field and submit it. Once you receive the ITIN, send the details to CA tax office to update the details.

That's correct -- unfortunately, you'll need to mail in your paper return.

Per California's 2019 540 Forms and Instructions Personal Income Tax Booklet, if your tax return has an amount due, mail your California tax return to:

FRANCHISE TAX BOARD

PO BOX 942867

SACRAMENTO CA 94267-0001

If your tax return shows a refund or no amount due, mail your tax return to the following address:

FRANCHISE TAX BOARD

PO BOX 942840

SACRAMENTO CA 94240-0001

I recently got my spouse's ITIN. Do I need to amend my state tax return on turbo-tax and re-print it? Or can I just write it on the previously printed return?

If you have NOT filed the CA return you can :

1) open the program, add the new number and reprint the CA return to mail 

OR  

2) just enter the number on the already printed return to mail  

Your choice. 

Thank you.

I am afraid, I do not see any box to fill in my spouse's ITIN on Form-540. Only on Form-1040, I see a box for spouse's ITIN.

Is Form-1040 the only form where I need to add ITIN, or is there some box on Form-540 as well?

Not sure how you cannot see that place ... it goes right under your number  ....  but you can open the program ... edit the spouse in the MY INFO section then revisit the state interview to bring the ITIN into place.

Since I already finalized and printed my returns, I cannot edit my info on turbotax. Looks like I have to write the ITIN on the printed return. And on the printed state tax-return I realized that there is no box for my spouse's ITIN (this makes it hard to locate), it just shows 000-00-000 against my spouse SSN/ITN. 

Thanks critter for all your help, just one last thing to confirm (since I am not able to edit info on TurboTax online) is there only one place where I need to write my spouse's ITIN on Form-540?

(So difficult to locate since there is no explicit box mentioning my spouse's ITIN, just 000-00-000)

You CAN EDIT the return ... here is the trick ... log in and scroll down and click on ADD A STATE to open the account.  

@JohnW222 Hello John, I would just like to confirm. Should I mail my state tax return without an ITIN and then mail another one once the IRS has issued an ITIN for my wife, or should I just wait? I'm also filing jointly for CA.

WAIT for the ITIN to come to file any state returns.  Put the state on extension until you get the ITIN.  NEVER try to file 2 returns as this will cause a mess. 

I filed my Missouri refund with "Applied for" itin for my wife as I was told by HR block representatives and I have received substantially less return. 

Should I file amended Missouri return after I get ITIN ? 

Yes.  You should file an amended return when you receive your spouse's ITIN.  State in the reason for amending "to report spouse's issued ITIN and to claim tax benefits not previously available due to lack of tax ID number."

When you filed extension and paid with CA 3519 through FTB online, what did you put in for your spouse's SSN while awaiting for her ITIN?

Hold off submitting the state return until you receive the ITIN then mail in or file return electronically