I'd seriously recommend you have a tank for your fry only.. it doesn't have to be anything big and expensive, a 1-3 gallon plastic tank would work fine.. the fact that your Molly-Fry don't go down to eat at the bottom is because of the Frogs, but Mollies at any age are enthusiastic bottom feeders and in fact do a pretty good job of helping keep the bottom of your tank clean between feedings (along with any Cories, Plecos, Catfish, or Loaches you may have).. fry require more feeding-times daily than mature fish, but since that's difficult to do unless you're home everyday all day, they will head to the bottom to feed when they're hungry in between the times you feed them, so it's better for them if they have no competion at the bottom at those times.. as for your sick fry, that's a tough one, the only thing I've ever been able to cure on fry is
ICH.. but ailments that require them to eat something like a pea will require you serving a portion in such a way that it's small enough for their small mouths.