Congratulations on your upcoming brood! We let our male release his first 3 broods in the main reef, and we lost most of them to predators. Still, use a turkey baster or 1/2" siphon hose (that's what we used) to pull the babies out - you won't be able to net them once they figure out what's going on. Since your baby tank won't be cycled, prepare to do lots of water changes.
We ultimately set up a 29 where Dad releases the babies, and then gets fattened up. The babies have plenty of hiding places in the LR, and have a fake urchin to hide in. (it's a full reef, with lots of softies who love the food the babies miss) The last brood he released in the "baby" tank was 40, and there are still 17 in there. (he ate some, but we also haven't bothered to put him back in the main reef - he seems quite happy now, and the babies are too big to eat now.) Watch your powerheads too - we lost a couple to the minijets. Fine mesh will prevent this, or you could just look at it as natural selection. You will have to clean the mesh off daily, though. Just an option, but less important to worry about at this point.
We feed enriched
baby brine shrimp from day one, and their little bellies will turn red (so you know they're eating.) We found that you can wait a day or so before feeding, if you mis-calculate and don't have BBS around yet. Enriching it with selcon is good, too.
Something else to consider, is that BBS doesn't have all of the nutrients babies need to develop complete nervous systems. This is why the baby-banggai-heart-attack-thing happens. Try to get them weaned over to better foods, and your results will be much better. (At least , it worked for us.) I feed PE Mysis that has been mangled into miniscule pieces by scraping it off the frozen block - it's small enough for them to eat that way.
TDW is absolutely right about the urchin. We have 2 Diademas (little ones) in the big reef, but they can be unpredictable. Better to get some reef-safe epoxy, form a ball, and stick lots of toothpicks in it. Stick it in the reef, and the babies will go right for it. Then you'll be able to find them to suck them out.
HTH and good luck! (They're so cute!)
Danielle