Ok I looked in my fish tank about 2 hours ago and there was 3 Guppy fry in there as well as my 3 neon tetras and 4 guppies and I was wondering will the other fish eat them if I have all large stones on the bottom which, I have seen the fry can fit under and the other fish can't. So will they still get eaten?

Yes. I had Guppies, all they did was mate, have babies, eat their babies and poop. Lol sorry, but it's always best to keep male and female separated. They will continuosly reproduce, and then eat their young.

If you want to breed guppies (and yes, it will happen again, Guppies breed like well... guppies) you need to get a breeding trap.
There are 2 types of breeding traps, one is a rigid trap, the other is a net.
You want the solid type NOT the net.
The solid breeding trap has a special compartment at the bottom that allows the fry to fall through to safety where the mother can't eat them. With breeding nets the babies are just swimming around with the mother waiting to become food.

You will also need special fry food.
It is available at most pet stores and looks like just a milky liquid. It contains food particles small enough for the babies to eat as they cannot fit regular food (even crushed) into their mouths.

Good luck, I haven't bred guppies in a while but all I did was use a trap and fry food and I had a tank full of healthy adult guppies in no time.