I have a garden in san mateo, ca that is only 5x9 and we have 5 large tomato plants, herbs, broccoli and lettuce. We have an automatic water sprinkler that goes off every other day. I want to know if I should arrange the time of watering to late morning or noon, it's set for 3am now. How low can the temperature go before covering and for how long do I do this? All winter?
I would begin watering the garden in the morning this late in the season. The reason for this is the cooler temperatures and moister air of fall and winter tend to favor fungal growth, so watering in the middle of the night, as you are now, keeps the plants wet for hours before the warmer temps in the day can dry them out. This increases your risk of losing them to blight or mold.
Tomatoes are heat-loving plants, and begin to fade and sulk when consistently exposed to temperatures in the 40s. So, if your nighttime temps there are hitting those kind of lows, I'd cover them soon and keep them well covered. I don't know what your winter lows are there or how well you plan to protect the tomatoes, but at some point this winter the plants may begin to become damaged by the cold even if covered. I'd keep an eye on your expected low temperatures and harvest any full size (or close to full size) tomatoes before any hard freezes. You can then ripen them at room temperature in the house.
The cooler temps won't upset the broccoli or lettuce - they actually like cooler temperatures anyway, but if you expect hard freezes then they should be covered as well for leaf protection. On how to treat the herbs, it really depends on what types of herbs you are growing. Basil, for instance, hates cool temps and will turn brown and be more susceptible to various wilts and rots once the night time lows begin to dip into the 40s. Parsley and cilantro, however, like cool temps and will do fine with just light protection during much of the winter. Thyme, sage and many other woody herbs are perennial and fairly hardy, so don't really need to be covered. Rosemary can be marginal in some areas, but if you are Zone 8 or warmer, it should be fine outside in the open uncovered.