Was your federal return accepted with a substitute Form 4852? Can you check your e-file status and confirm - it should have been rejected... If it was accepted, that is a new thing because you have never been able to e-file with that form, see this FAQ. I don't know if it will take your payment for an e-filing fee. But if you can't e-file, don't pay the fee. You may have to jump through a few hoops to get it refunded.
On the 2nd question, yes, paying directly at the FTB is your best option. If you mail the return, you have to include all of your forms, but you do not need to include any payment or payment information. There will be an instruction sheet when you print that lists everything you need to send. If you pay online, you get an instant receipt. If you send a check, you are left in limbo for too long, in my opinion anyway.
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