First of all, ignore the clerk. He is wrong. Half of what they tell you in traffic court is wrong. The bailiff will probably tell you before the judge comes in that you can only plead guilty, not guilty, or no contest. Wrong. It amazes me that they force you to listen to legal advice from non-lawyers, but they do.
When you go to the arraignment, you are quite within your rights to not enter any plea at all. The Vehicle Code gives you that right. Or you can more specifically say you wish to demur.
If you say you demur, then by law the judge is supposed to hear your demurrer immediately. But being the scofflaws that they are, they won't hear it immediately. They will give you a date to come back for a hearing, because that suits them better, which is more important to them than following the law.
So you will have to go to court twice - once for the arraignment, and then again after probably 30 days for a hearing on your demurrer.
Filing your motion and serving it can all be done by mail.
Demurrer motions can be found all over the internet, or I can send you one. If you want to use the mailing envelope at your demurrer hearing, you should consider serving notice on the DA that you intend to that. I had another thread on this forum that outlines how to do that, and you should include the case that I mentioned so that the judge knows he needs to accept your evidence. If you don't do that, the judge might not admit the evidence (some judges think, incorrectly, that they are only allowed to look at the complaint itself, and nothing else, at a demurrer).
You are definitely in for a little bit of paper-shuffling and court-attending, but the fine is $500 so it's worth doing.