In most states, as I'm fairly sure is the case with California, you would register as a foreign entity in California, and would pay taxes in California relative to the income produced in California. Which, if you were a Delware Corporation with all of your resources in California, would be 100%.

Edit: Here's your California SOS FAQ on the subject: http://www.sos.ca.gov/business/be/faqs.htm#form-question7

If you want to open a business bank account in California, you need paperwork from the California Secretary of State. HSBC, Chase, Wells Fargo all asked for it. If someone managed to get an account without the paperwork, I'd like to know where.

You pay a "franchise tax" to whatever state you actually operate in, regardless of where you are incorporated.

Thus, if you are incorporated in Delaware but based out of California, you would be subject to taxation in both Delaware and California.