My swordtail fry (similar to mollies and platies) ate crushed flakes as well as Hikari First Bites. My first batch died. They only got the flakes. The second batch however survived; I fed them the flakes and the Bites.
Since you're already close or at your stocking limit (how many fish you can put in your tank), you probably won't have enough room to raise the fry. They need to be away from their parents until they can no longer fit in fish mouths. So either you get another tank (they can't grow up in that breeder container thing) or you feed them to your fish...
I'm assuming you didn't cycle your tank?
When you first get a tank, you have to cycle it, as in, establish bacteria. And putting in all six fish at once (if you did) is probably going to stress them out.
The mollie either died of giving birth or being stressed out by something.
If you don't have a water test kit yet, you should get one. The liquid tests are more reliable than the strip test.
Freshwater and Saltwater Aquarium Supplies at AquariumGuys.com has a cheap one (cheaper than Petco and Petsmart.) API Freshwater Master Test Kit is what I use. That'll test for ammonia (not good), nitrates (good to a certain level), nitrites (not good), and pH (as long as it's stable, you're fine.)
Good luck and welcome to the tank!