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