I am so sorry that your son was diagnosed with this. I remember feeling overwhelmed when my daughter was diagnosed with 1 food allergy. I can only imagine your angst at facing numerous allergies!
Here are my ideas... It's late so sorry if long and I ramble:
My first suggestion is to buy a bread machine, one that can make bread as well as jam, pizza/pasta dough, cookie dough, cake, etc. You're going to have to homecook most items since soy is inso much pre-made food. You'll need tools/appliances to help you do it quickly. I bought the Zojirushi brand bread machine from Amazon.
I also use a popsicle maker (bought from Williams-Sonoma). It was a little pricy, but since one of your children can't have real ice-cream and the other can't have soy ice cream, fancy homemade popsicles that freeze in 9 minutes might be a solution for you.
You should start googling recipes that use flour from potato, barley, oat and rice. You can make bread and pasta with barley, oat and potato flour, so you can make him sandwiches and noodles (most store bought bread/pasta has soy). You might need to experiment with recipes that call for wheat and substitute with other flour types.
My daughter has a milk allergy like your other son, however she can eat goat diary. I mention goat dairy for 2 reasons: 1.) many recipes require a fat ingredient in order for the recipe to work correctly. A lot of processed food is replacing dairy fat with soy (soy is cheaper than dairy). However, since your son is allergic to soy, that will wipe out a majority of commercial pre-made food that use vegetable and saffola oil. I am assuming you will homecook with goat butter, olive oil or canola oil instead? 2.). Since you don't want to prepare multiple items to appease each son's diet, if your son that is allergic to cows milk dairy can eat goat dairy then you should be able to cook with goat milk/butter/yogurt for everyone-?
Like bread needs milk and butter in the ingredients in order for the crust to be squishy; French bread isnt made with milk/butter, but the crust isnt squishy (although commercial french bread seems to be made with soy lechin; homemade doesnt have soy). If both your sons can tolerate goat milk & goat butter, then you won't have to have one loaf of bread for one and another for the other.
For on-the-go commercial snacks, here are a few ideas:
Apple sauce
Dole fruit cups
Rice cakes
Rice crackers & rice cookies (check out the Asian food section in your grocery store)
Fruit leather
Freeze-dried peas, strawberries & bananas (my daughter loves these! Made by Just Tomatoes. Check out www.justtomatoes.com)
Almond butter & jam for PB&J sandwich.
Your son with multiple allergies can have cows milk dairy, right? So at least he can have yogurt, string cheese, cottage cheese, etc.