If you filed a Joint Federal return, you could also file a Joint Non-Resident CA return. You would report only your CA income and CA tax paid.
However, if you want to file a Separate CA return, you need to prepare a Separate Federal return first, as the data flows from the Federal return to the state return.
Here's instructions on how to do that:
https://ttlc.intuit.com/replies/3301995
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