I use shoebox sized tubs, just the cheap $1 ones.

I put light diffuser on top of the substrate and I don't use any press-n-seal or anything like that.

I also don't poke holes in the tub, they will breathe as long as you get the cheap tubs, those are no where near air tight.

And I leave the eggs in the same tub when I cut them. They will be just fine. Once they come out of the egg I replace the substrate with wet paper towels and leave them all in the same tub in the incubator until they all shed.