I've done both ways with similar results. Most of the time, the fry will be strong enough to hold off any fungal infections. Clean water is a necessity for it to not be a problem tho. I suggest that if you start to see some fry turning white, I'd remove those fry and try to remove as much of the fungused eggs as well. I use a piece of rigid tubing attached to a long piece of airline tubing so that I can suck the infected areas into the rigid tubing for removal. ( Just don't suck too hard to create a siphoning effect.
) Make the rigid tubing long enough so that you can get to anything on the bottom of the tank.
( This setup will also help when you start feeding the fry and there is leftover food. You'll want to remove any excess food before it pollutes the water.