Yep, new media in a filter basically means a new filter. If you take a handful of gravel from your tank, put it into a net and place that in his tank, it'll help kick start his bacteria colony. Then can take your gravel back once it's cycled. Add some fish food to the water and allow it to degrade, which will produce ammonia for the BB to feed on and grow the BB colony. Have a read of those threads Salty linked about how to cycle a tank. One or two adult mollies can help make sure it stays cycled once it's safe enough to put them in, until you're ready to add to the fry.
For the fry, if you can get some floating plants, and or some fast growing stem plants like hornwort or anacharis and leave that floating in the main tank/new tank, it will not only help take up ammonia and nitrates, but give the fry a good hiding place and gives them a better chance of not getting eaten.
My molly, platy and guppy fry stay in the tanks with the adults from birth. Heavy planting and a lot of stem plants/floating plants gives them a good place to hide, and tanks are well fed enough that the adults aren't hungry enough to be actively hunting for fry. The stem plants that I leave floating in a 55 gal are packed full of fry, who stay in thee like a nursery until they're big enough to venture out safely. They make it, even with big mollies and a gourami around. I feed the adult fish on one side of the tank, then crush some flakes into tiny pieces for the fry in the plant nursery. Tiny frozen or live food like cyclops, dahnia and baby brine shrimp are also great since it floats around in the water column, and fry don't have to come out and risk being chased by adults to eat.
Not the end of the world to me if some of them get eaten, since more than enough survive. Of course, keeping the tank of adults well fed means more water changes to keep the water levels healthy.
