This is a little late, sorry. I feed my guppy fry crushed flake food and I don't seperate them from any of the fish. If you have plenty of hiding spots, they will survive. I have atleast 60 guppy's in my 28 gallon tank now. (Just a little over stocked. LOL). I don't use breeding nets or contrations, I just let nature take it's course. I had only 3 guppy's a year ago when I started this tank. I also feed them to other fish, so I have had PLENTY of fry in the mean time.
In all honestly, I find guppy's to be my favorite fish. You just never know what colors you are going to have from day to day as the fry grow up.
I hope all is going well.