As far as general guidelines, bettas should be kept around 78-80 degrees Fahrenheit, fed a mixed diet consisting of a good quality pellet and frozen foods such as bloodworms, brine shrimp, daphnia, etc. (you could also use live, but many prefer the frozen because there is less chance of disease), and prefer slightly acidic water - that being said, they can adapt to a wide range of pH values so long as it is stable. They do need access to the surface to breath, so leave the water line about a quarter inch below the lip of the bowls. Since they can (and do) jump, covering the bowls is essential, and this will also trap in the heat better and warm the air above the water's surface, which is preferable for them to breathe.
I think perhaps the most important thing you can do for these guys is to give them some heated, clean (you may need to do daily, 100% water changes if the bowls are small) water. Do you have at least one spare heater? Until you can get proper setups for them, one way to heat them is to float all the bowls in a larger, heated container (a large rubbermaid bin works nicely). Or, since you have reptiles, perhaps you have some heated tape that you could run under the bowls?
Live, silk, and some plastic plants (provided they aren't sharp) work fine for bettas, and terracotta pots make nice cheap hiding spaces (just make sure to plug the bottom hole). I just wouldn't put live plants in with any fish you will be medicating.
I wish you the best of luck with these guys... I agree that it is absolutely appalling how they are treated in these stores. I realize that bettas must be separated due to aggression, but that is no excuse for blatant abuse and neglect. Bettas could easily be kept in larger containers on a shelf with some heated tape attached to a thermostat, and given good food and daily water changes. Even if the store did make a profit from your purchases, you have accomplished something really special: you taught your son that this treatment of living beings is not ok, and that is perhaps the most important aspect of improving the treatment of these fish in the future :)
If you run into specific health problems with these very lucky fish, feel free to ask! Good luck!
20 gallon long: 3 adult Neolamprologus similis + about 11 fry of various ages; low light planted tank
20 gallon long:2 freshwater dwarf puffers (Puff Puff and Poofer); medium-light planted tank
10 gallon: 1 male betta named Wormy; low light planted tank
10 gallon: 1 male betta named Dante; low light planted tank
2, 5.5 gallon tanks that are currently empty (I see more fish on the horizon