At this moment in time, I have roughly 250 baby sailfin mollies, from a total of 4 spawnings...be careful what you wish for!
I have acclimated both sets of my parents to saltwater so except for the first batch, the rest were all born in full salt. Other then that, there should be no difference in raising the fry. I would definitely keep them seperated. I took a mortar and pestle and ground up a spirulina based fish food for them and I feed them twice a day. I have sponge over the filter intakes and this works well to keep them from being sucked into the filter. You might want to check your filter for living babies...it happens quite easily and you may have some in there. Be sure to rinse this sponge every few days or your water flow will just bog down.
is one of the threads with the story of my baby mollies..if you are interested.