When I had the fry I used a plastic breeder. Mine didnt have large slots however so this wasn't a problem. I found it better because with the net breeder there is always the chance that fish can try and suck them through. Obviously they won't actually get them through but they can hurt them trying. Depending on what fish you have however this may not be a problem. Id you're really worried you could possibly put the net breeder inside the plastic breeder, or vice versa and just keep a really close eye on them. I'm not sure how this would work with sizes thoguh as I've never had a net breeder myself.
If you do deicde to use the plastic one, maybe in a few days when they're a bit bigger, just remember to "change the water" daily. I just slowly lifted the breeder out of the water until there wasn't much left (very slowly and gently so as not to disturb them) and back down again to let the water come back in. Plastic breeders don't allow for much circulation.
I think you were right not to put them in the other tank. Babies are very sensitive to any params that go off, even though thy might not be harmful, any deviation from their original conditions can be harmful from what I've read. I wouldn't want to take the chance. In a few weeks I would move them if you can get the filter sorted as the more room they have, the better they will grow.
For food I used egg yolk for the first few days and they seemed to enjoy it. Just a tiny pinch in the water, crumbled and then squirted into them with a pipette. After a few days I couldn't find any baby brine shrimp so what I used was a combination of the egg yolk, crushed flakes and freeze dried brineshrimp. It was the sort that came in a sort of jelly and I broke this up along with some water and fed it like it was the egg yolk and they took it very well.
A llink to my post from when I had the fry, which was a real learning experience for me is here: http://www.fishforum.com/viewtopic.php?t=6280
. A few folk have said they found it quite helpful so I hope you will too.
If you've any other questions just post them, or pm me, whatever and I'll try and help you the best I can.