You can use a carpool lane for free almost all the way up and down the 5 freeway. All you need is minimum of 2 people in the car. The carpool lane is in effect 24 hours/day and is the far left lane, dennoted by diamond shapes. Please be aware that you need to drive at LEAST the speed limit when you are in there, which is 70mph most of the time. If you don't push it to around 80, people behind you will tailgate and eventually swerve around you in the openings. Only enter and exit in designated areas (don't cross the solid lines at any time). Ticket fines are VERY high if you get pulled over for violating carpool lane rules.
The toll roads in Southern CA are transponder less. If you use one, you go online within 5 days to pay. You need to know where you entered and exited. If you do not pay online, you will get a bill in the mail and are allowed a one time grace on paying online. The second time you fail to pay online, you are assessed a $50 fine. There are some toll roads between SD and Anaheim, but none will take you the way you are trying to go. The most direct route is I-5.
I think there may be some fasttrack lanes once you get to San Diego, but they lead away from the port.