The Total Amount option requires that you allocate that portion of the gain you received while a non-resident of California and that portion of the gain you received while a resident of CA. You may have already seen this, but if you select Total Amount, on the screen, Allocating Capital Gain or Loss is where you enter the applicable allocation amounts.
The other option as you noted is Sale by Sale. If you select Sale by Sale, you will not see a screen where you are specifically asked to enter your allocation amounts but rather, you will see the screen, Capital Gain and Loss Summary. It is here where you can Edit the listed entries to allocate gain/loss to CA sources.
Ordinarily, when taxpayers are provided with two--legitimate--ways of computing the tax, the standard reply is to select the option with the best tax outcome. However, in your situation, the issue you are addressing has to do with allocation of gain/loss to CA. Whichever option you choose, Sale by Sale or Total Amount, the result should be the same. In other words, with either option you are taking your gain and allocating it to CA for the period of time you were a resident versus the time you were a non-resident. From a tax perspective, the result should be the same.
What are the differences you are seeing, and can you tell the reason why you are seeing different tax outcomes? Follow-up with any additional information you feel may be helpful.
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