You need to find and close the opening they are using to get in.

You'll have to find out what they are before you can decide just what you are going to do about it. It may require some stalking on your part.

An experienced pest control company would be able to inspect the site and identify the critters, too.

As an addendum, you should know that poisoning bats (I don't know about flying squirrels) is illegal to say nothing about dangerous. Exclusion is your best (perhaps only) option whether the culprits are birds or mammals.

But you'll need to know the habits of the animals in question. You don't want to exclude all of the adults from returning to a nesting site, when there are many babies left unattended to die.

The place where I worked had a barn infested by bats and it was causing serious debris problems in a space we wanted to use for people. One night, we set up a watch all around the barn at the time when the bats came out. We were able to identify where the holes were that the bats were getting into. Then, another night after the bats left, we sealed the holes. End of problem. Killing whatever it is--bats, birds, squirrels, etc., and not sealing the holes where they are getting in will not solve the problem since new pests will just come in to replace the ones you killed. It's a bit of a pain to do this, but this is what you need to do to really solve your problem for good. Find out what it is and where it is getting in and out. Then you can come up with an effective solution.