Even though this discussion thread deals with 2018, it seems to be the best.  So I'm going to add some notes that apply to 2020 and 2019.

1.  The biggest issue I had in getting the right answer is that the 540-ES worksheet was active from the original return.  You should deactivate it for the amended return.  I did this by checking boxes Part I 3a and Part II 2b.  Otherwise, the amended return may try to apply some of the overpayment to the next tax year.

2.  Form 8879 (CA) is not correct.  Line 2 & 3 have amounts from form 540 but should have amounts from Schedule X.  See 8879 (CA) instructions.  You'll have to override these values.

3.  If you have a balance due, the program (and I think FTB) do not support electronic withdrawal from the program.  

4.  Form 3582X Payment Voucher is not supported.  This will have to be completed by hand.  Note, that Drake supports this form.  Another reason to consider Drake next year.

5.  TBD - Electronic deposit of refund.  IRS does not support it.  FTB does (per 8879 (CA) instructions).  Not clear that ProSeries does.