uhhh... if you plead not-guilty, you are sent a letter about a month or two later, asking you if your SURE you want to plead not-guilty.
If you do end up pleading not-guilty, another 2 months later you receive your court date. Whether you go to court or not, (considering you lose) your going to have to pay an extra $50 for court fees. However should you win, you don't have to pay those court fees, or the fine. But in some cases, like one that I had, they may find you partially guilty. I had run the stop I knew that, but my defense was that I slid through. It was a little icy out that day. The judge accepted that, but said that in those conditions, I should be braking earlier, and instead of paying the full fine, I only had to pay a partial amount.
What I would suggest is pleading not guilty, and then when they send the confirmation back to you, to make sure, change it to guilty and pay the fine. It'll take roughly 2 months.