Here's the site: http://www.sdmts.com/trolley/trolley.asp
If you're in Downtown San Diego, the Santa Fe Depot is the old (historic?) train station from which you can start.
Enjoy the trip!
You can park on the US side of the border in San Yisdro and walk across the border to Tijuana for some tacos and stuff, and then walk back. If you don't have access to a car, you can take their light-rail metro system from downtown San Diego all the way down to San Ysidro and walk across too.
There's not much to see there though, and some people still consider it a little dangerous (especially at night). You can also hail a taxi directly across the border and take it down to Rosarito or Ensenada for an afternoon day trip. Both are a bit less hectic than Tijuana, and a taxi ride shouldn't cost more than like $30 each way or so.