I can't help you regarding the travel questions, but I'll do my best with the rest!
You'll need to go to the hotel to pick up your park tickets, if you don't have the express check in, you don't really have a choice. It may be worth trying to call Disney again and ask them if you can add the service. Otherwise I suggest when you come out of the station, you go straight to the shuttle buses (you'll see the bus station when you come out), and take the bus to the hotel. It only takes a few minutes, you can leave the bags there (if you're lucky your room may even be ready), and collect your park tickets. You can take the bus back, or walk to the parks (it's a nice walk, by the lake and across the Disney Village
If you have your park tickets already with you, you can leave the bags in the station (there's a luggage service place, not too expensive), and collect them later.
Breakfast can be a fit of a bun fight... When you check in you'll be asked to choose your breakfast time. The rule is, try to go as early as possible (7am is the best) to avoid the queues. Other options in the Disney Village are Cafe Mickey for a breakfast with the characters (you need to book it in advance), Starbucks, Annette's, and even MacDonalds.
If your little boy has a good appetite, best places to eat are the buffets - children under 3 don't pay, and you'll find plenty of choice in all buffets! My personal favorite is Agrabah Cafe (lovely Mediterranean food, a great starters buffet, and great theming). Plaza Gardens is also very nice (more continental food, and a great desserts selection). In the Studios you'll find the Restaurant des Stars (food selection is similar to Plaza Gardens, but here you can meet Remy from Ratatouille). We went a couple of months with our 2 year old and we found buffets worked best for lunch (in the evening she was tired and not too hungry, so I usually just gave her a ready meal).
You can have a look at restaurants (and menus)
here.
We also found character meals a great way for our little one to meet the characters without any fuss. Of course once she saw Mickey was around she didn't eat too much, she was busy following his every more and waiting for him to come over to see her, but still... Really worth it.
By the way characters can be quite intimidating first time, our little one is a huge Mickey fan so she was only too happy to meet him, but I've been plenty of times with other children who were a bit scared at first... So maybe wait a couple of days before trying to see them up close and personal, and start seeing them from a distance in the parades and shows first...
In terms of rides, our little one loved Buzz Lightyear (try to do it first thing in the morning, during the EMH, or use the fastpass during the day to avoid the long queues), Peter Pan, and It's a Small World. Most rides in Fantasyland are suitable for little ones (though I find Snow White can be a bit scary for some children). In Adventureland we did Pirates of the Caribbean (not her favorite ride, but she still enjoyed it). You can also go around the caves and try to find the buried treasure! In the Studios you have to see Animagique (a stage show with Donald). Our little one also enjoyed Playhouse Disney, the flying carpets, and the slinky dog ride.
You also have a couple of playgrounds for children to run around, with slides and all. My favourite is the
Pocahontas Village in Frontierland, and there's also another one in Adventureland, by Captain's Hook galley.
I fear the parks will be quite busy when you're there. Since you have 5 days you can just relax and not rush, and do what you can. We found that a full day in the park was too much for our little one; for us it was best when we went back to our room for her nap, and going back early evening into the parks. You may find that the park is busiest after 11-12, and until 6-7 in the evening.
You can go to Sea Life in Val d'Europe (ask in the hotel, they sometimes have a shuttle service from the parks to the Val d'Europe shopping center). You also have a nice pool in the hotel (including an outside bit), it could be a nice way to spend the afternoon!!
I'm very bad when it comes to spending in Disney, I confess... For meals, buffets start around the 20-25 euro (and children under 3 don't pay). Menus in the fast food places are around 10-15 euro. And a menu (starter + main course) at a table service restaurant starts around 30 euro. Then there's souvenirs, snacks during the day...
Hope this helps a bit!
Have a magical time
