Pat has some good route advice. I live in the Bay Area and ride the Santa Cruz Mountains often and can add bit more.
ANY road over the mountains is much busier during commute hours. There is a heavy flow each way but local riders know to stay off these roads going either direction during commute hours as the roads are very twisty and the people drive WAY too fast. I stay clear after 3pm to avoid the high school drivers too.
Having said that my favorite route over the hill is from Los Gatos to Watsonville. Join the Los Gatos Creek Trail (it starts in San Jose) and take it up to Lexington Reservoir. There's a 2 mile segment of packed gravel road. Follow the East side of the reservoir, Alma Bridge Road, to join Old Santa Cruz Highway, Left at Summit Rd/Highland Rd. (this road had a washout and was closed for some time last winter so check that it's open) then, my favorite, Eureka Canyon Rd. to Watsonville. Beautiful and once on Highland Rd. very quiet.