It's more than a couple miles so you will want to use a Cab. Maybe ART but it might be complicated and take a while.
As an option don't feel locked into Amtrak. At the SD station and more in the SD area is the Coaster, it runs every 30 minutes during the day. It will require a transfer to the Metro in Oceanside to go up to Anaheim. The Metro also runs every thirty minutes during the day.