To prevent fry from being sucked up a filter, you can cover the intake with pantyhose or sponge, or jam a sponge down it to partially block the flow.
To help more fry survive without being eaten, there are a few different options. You can either make sure you have lots of hiding places like decorations or plants where a baby can hide from other fish, or you can put the fry in a fry trap. Fry trap will get you the most babies that don't get eaten, and it will also take care of the filter problem. If you go for the fry trap, you can either put the female in the trap right before she has babies, or you can wait and try to move the fry into the trap after they have been born.
Baby guppies are big enough to eat really finely crushed flake foods, or you can specifically get them smaller foods.