I've been doing water changes twice a day before feeding to be on the safe side. I haven't actually taken the fry out yet so not quite 100% changes but have taken everything else out to give the bottom a good Hoover and used the turkey baster. I shift the moss around a bit to suck up some bits from underneath if I don't take it out. Maybe if you wanted to change water twice a day you could do one 100% like you have been doing and one with the turkey baster? Saves taking the fry out twice then.
Mine have pretty much just had microworms, moss, and some water from the top of the filter with a few bits in so far. Because the worms live for 24 hours I'm not too worried about the water quality as I'm doing a water change every 12 hours or so anyway. If I was using anything that wasn't live I'd be a bit more worried, like I was after the brine shrimp that only live for 5 hours. I'll be much more careful about how much of that I put in next time. Hopefully the fry will be big enough to go in the breeder box in a few days and then I'll start some dry food and frozen cyclops as there will be a bit of water flowing through from the main tank too. I'm sure I'll be doing the water 'exchanges' more often then though like Eagles suggested to be safe with the food not being live.