As the female who laid this clutch of eggs was ill and calcium deficient (it would have been better not to breed her at all if she was already sick, unless she was bred before you got her) that would be the main reason the eggs didn't develop well. It is good you are getting some hatching now.
Baby bearded dragons are fine in a small cage once their egg yolk is absorbed and don't need to be offered food for a few days. After a couple days, offer 1/8th inch crickets (pinheads), small phoenix worms and very finely chopped greens (probably won't eat these at all but some will so it won't hurt). Keep them very well hydrated with frequent misting (don't mist the cage heavily though, a spurt or two on the dragon and maybe the side of the cage is fine). Once they are eating, offer food 3-5 times a day spread out every 2-3 hours. Dust with calcium powder as BDLvr suggested above.
For the two year old female, once she's out of quarantine with a clean fecal from a vet (one month is ok, though three months is better with three clean fecals to make sure all is well). Then you can start preparing to breed her for the new season. It may be a bit later than others, but best to have a healthy parasite clean pair of dragons than to rush too soon only to have one get sick or suffer problems during or after laying eggs. Brumation may also be needed to get both dragons fully 'primed' for breeding.
BDLvr and others here have alot more experience breeding dragons than I do. I pretty much know things from reading but experience has its value as well.
For incubation, the hova-bators are fine, just don't use the models with the fan. You should be able to disable or just remove the fan in your current incubator. Vermiculite is fine as an incubation medium as long as its moist enough without being too moist. Perlite can be used as well or even a mix of the two. Just measure the medium and water by weight, not volume, and shouldn't be any problems. For bearded dragons I think its a 1:1 ratio by weight of medium and water. OR dampen so you can squeeze the medium hard without any drops of water coming out, but it clumps together nicely.
Also remember that a healthy female bearded dragon can easily lay 3-5 clutches a season, with each clutch being laid 3-4 weeks apart on average. Some bearded dragons have lain clutches barely two weeks apart. So always be prepared to toss in the egg laying bin for your female to lay her eggs. Use frequent dusting of calcium without vitamin A or phosphorus, use a good UVB bulb or an hour of sunlight a day (direct sunlight, not filtered through glass, basically take her outside for natural sunlight several times a week for an hour or so, weather permitting).
If she stresses alot when being taken outside, then best to just stick with a good UVB bulb.
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PHLdyPayne