Thank you all for the information. I booked Business Class to hopefully improve our chances of a comfy ride. I find the more prepared I am with 3 kids, the smoother things flow and it's the getting to and fro that requires the most organization. I'll definitely take a look at the videos you suggested BCLA - this sounds very similar to how our commuter train system works here in Toronto. And thanks for the tips Suzanne. Much appreciated.
The first vid seems to be of a group entering a California Car painted in the Surfliner color scheme. The seats seem a little bit different than I've seen riding the Capitol Corridor or San Joaquin, but otherwise the layout seems to be the same. These cars have two doors on each side and are pretty much all open together when the conductor presses a button to open them. They're linked to open together, and the conductor only has to be at a door with a control panel, which is active when the conductor turns a key (you'll hear conductors walking around carrying several keys making tons of noise).
The doors can also be opened individually, which appears to be the case in the second vid. That's still a coach car with two doors, and the passengers are walking by one of the closed doors.
Some of the Pacific Surfliner cars are retrofitted Amtrak Superliner cars with only a single door on each side (at the center of the car) that can only be opened if the conductor is specifically at that door and presses a button at that door's control panel.
I wouldn't stress it out too much. Different crews adopt different procedures, so be flexible. Even if you can't find seats together, ask if a conductor can help you. If they tell someone else to move, they are required to move or they can be removed forcibly if necessary.
Additionally, the most that can really sit together is four (maybe five if the 2 yo sits on a lap), so you might want to be flexible and accept a table or four facing seats, plus a couple of seats together. Someone noted that it can be even more crowded in business class than coach. It's just that they won't sell more reserved tickets than they have seats, but in coach it's possible to use an unexpired (one year to use) ticket, buy a ticket on board with a penalty (depending on the station - some don't have ticket sales and there's no penalty to buy on board), or use a 10-ride ticket or monthly pass. There are no guarantees that business class will be less crowded than coach.