Well if the mom has a history of eating them then it might be wise to keep her away. BUT sometimes new parents will do this. If it were me.. I think that I would put her in, but at the first sign of fry chomping I'd remove her. You'll have to watch closely to see if she is actually eating them or if shes just cleaning them. They will take them into the mouth and kinda swish em around and spit them back out to clean them. It is a very tough job running after that many fry for both parents.. the father probably could do it himself, but hes gonna wear down pretty quick and probably eat some to cut down his workload.
As for feeding the fry.... when they become free swimming, they yolks are more than likely gone and you can start BBS then. But dont fret too much because you said they are in a java fern roots and that is a wonderful place for them to be right now. Once they really become active is when you need to put in the BBS.
Question... you said divided tank. Hopefully the divider does not have holes? Are there other fish in the tank? What about your filtration, they can get sucked up if you do not put something over your intakes. I used a piece of nylon and a rubber band to hold it on to my filter intakes.
Amber