There's only one route for that pair, so I assume you're taking the overnight Coast Starlight to Martinez and then finishing the trip via bus for about an hour.
My first recommendation is to pack with the knowledge that you'll be on the bus! There's no checked baggage on the thru to Napa, so you'll be lugging it.
For the overnight portion of the trip I bring a small bag with at least:
- Night clothes
- Night slippers (really cheap $3 pair from IKEA)
- Needed medical items (CPAP)
- Tomorrow's change of sundries (briefs/socks) and a clean shirt.
- Small alarm clock/smart phone/computing tablet
- Toiletries to include toothbrush/paste and a hairbrush/comb
That bag gets chucked into the overhead bed the moment I hit the cabin and I forget about it 'til I need it. Most people don't realize that there is ample space in the top bunk for stowing things you won't need 'til later, but I've gotten so comfortable with at least the Roomette's that I've dropped the beds myself when I had a no-show attendant.
For the cabin during the day I pack a small backpack with
- a few pieces of fresh fruit (the one hard thing to obtain on the train)
- cocoa powder*
- some reading/writing material
- a card game or two**
- the camera for all that scenery you paid for
- personal portable music system (and the wall plug for said unit)
- the laptop (if you're that sort of person).
Amtrak does a good job of providing water, hot chocolate (see note below) and drip coffee to the sleepers. The snack car has boxed/canned foods similar to what the airlines sell now-a-days and the dining car will keep you fed at mealtimes. Since you're boarding after 9:30am, I don't think you get breakfast on day one, but lunch, dinner and the next morning's breakfast (if you are an early bird) will be included.
My wife and I love taking the train when we're not in a hurry. It gives us a chance to leave all of 'right now craziness' and just enjoy the day while the countryside passes us by.
Enjoy it!
* Amtrak usually provides packets of hot chocolate, but my experience is that whichever cabin has the kids in it usually ends up with all of the packets within minutes of departure, or at least within minutes of discovering them out by the hot water tap.
** We typically bring card games because they are compact and can be deployed onto the tiny tray tables in the sleepers. We'll often head to the observation/lounge car to play if we're not taking space away from others. We also tend to bring games others can join in on if they like, as we are always happy to teach a new game to fellow travellers.