You will be able to check in your bags at the station in San Diego and will receive claim checks that say Stockton on them for your bags. The actual bags will be tagged (by Amtrak staff) with a bright pink transfer slip that indicates the bags will be transferred over to the thruway bus to San Jose. The bags will be transported on the Surfliner train, San Joaquin thruway between Los Angeles and Bakersfield, and the San Joaquin train between Bakersfield and Stockton (all in secure, innaccesible baggage areas). At Stockton the bags will be taken off the train and brought over to the San Jose-bound thruway bus for you. You shouldn't have to worry about them; just give your Stockton claim checks to the thruway bus driver when boarding and he/she will make sure your bags are received and stored underneath the thruway. You will be able to get them when you disembark at San Jose.

Have a great trip and thank you for traveling Amtrak California!