Responses to your questions:
1) You need to look at what you expect the total California liability to be and make estimated tax payments based on that amount. See the attached link which provides some useful information <a rel="nofollow" target="_blank" href="
https://www.ftb.ca.gov/businesses/Structures/S-Corporations.shtml?WT.mc_id=Business_Forms_SCorpTOC">...>
2) I believe this is due to the incorrect registration. When you call the FTB they can hopefully provide some direction here.
3) Your question asks about income for "state taxes" and not specifically California. If you are asking about state taxation of S corporations in general, that will depend on each specific state. If you are asking about California specifically, I have attached a link to the form 100S for you to review <a rel="nofollow" target="_blank" href="
https://www.ftb.ca.gov/forms/2017/17_100s.pdf">https://www.ftb.ca.gov/forms/2017/17_100s.pdf</a>
4) And the booklet for the form 100S <a rel="nofollow" target="_blank" href="
https://www.ftb.ca.gov/forms/2017/17_100sbk.pdf">https://www.ftb.ca.gov/forms/2017/17_100sbk.pdf</a>
5) Keep in mind that each state passes their own legislation on whether or not they follow federal so most states have numerous state adjustments as a result. Depending on your business, it may be in your best interest to get some professional assistance in the beginning to make sure you get started on the right path.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
