Great choice for a run! The run along the coast between San Juan Capistrano and San Diego (through Oceanside) runs right along the beach and is great.

1) They are "reserved" but not pre-assigned. Coach seats are unreserved, meaning that they sell an unlimited number of tickets per train, and if more tickets are sold than seats are available, you're left standing. For business class, depending on the run, your business class attendant may assign you a seat upon boarding, or you can pick a seat yourself (it's usually the latter). The difference is that they limit the number of tickets sold for business class so it doesn't get oversold.

2) Theoretically, you can board two minutes before departure and be OK. Due to the logistics of wandering through Union Station and finding the track, I'd plan on arriving at Union Station at least 15-20 minutes before, and probably even earlier, since you're not super-familiar with Amtrak's procedures. (The earlier you arrive, the better seat selection you'll have upon boarding, too.)

3) The Quik-Trak machines are pretty self-explanatory. They're located on the wall to the right of the Amtrak ticket sales counter. Just have your reservation number available and you should be able to pull it up pretty quickly.

4) You'll want to sit on the right side of the train going down and the left side coming back for the best ocean views. For the direction you're going, when you get on the platform, take note of where the locomotive is. That's the front of the train, so make sure you orient yourself the right way to be seated on the correct side. (Also, half of the seats face forward and half face backward, so you might want to pick a forward-facing seat--again, pay attention to where the locomotive is.) Note that upon the return, the locomotive will be pushing the train, so pick your seat knowing that the train will be traveling in the opposite direction of the locomotive.

Have a great trip!