Please don't put the mother in a box, those tiny containers are very stressful for fish. It is much better to leave them in the main tank. If there is enough decor - preferably fine leaved live plants - fry will survive. I suspect the reason you only found one fry is that the rest have been eaten.
How big is the tank? Bettas are commonly kept in small tanks while mollies are big fish which need a big tank.
Do you have 2 females, or a male and a female?
Female mollies, like most common livebearers, can store sperm and use it for many months to have fry. If this molly has just had fry, she'll very likely have more in 4 to 6 weeks. And if the other molly is also female, she'll have fry at 4 to 6 week intervals as well.