Do you know what the real number one cause for frogs diseases is?
Stress.
Do you know what is stressfull to them?
Changing their substrate daily and cleaning of every single plant.
Come on.
If you overcrowd you're viv, i see why you wan't to do this.

But overcrowding is stressfull, so is handling or disturbing you're frogs and the environment this excessive .
With al due respect, but i totally disagree with the person that told you this is the best way of maintaining you're frogs.

If you keep the frogs in a tank large enough, live plants, normal substrate and some janitors like woodlice or springtails.
The waist will become plant food.
Once in a while you can take a damp paper towel to take of excessive waist from the leaves of the plants.
This will be way better then stressing them out this much.

Still, the problem of crossbreeding remains.
So i would really advise to keep them apart from eachother.
For poisoning i'm not afraid, since agalychnis isn't poisonous at all
I'm more afraid of you hurting you're frogs skin due to the acids from you're own skin or any residues from something stuck to you're hands.