Since you are not sure which cat it is both cats need to go to the vet for a check up ASAP. Usually pooping doesn't stem from a health problem as much as urination does, however.

If all is clear on the health front, then the problem is behavioral. You will need to take steps to retrain the cats to the box. Basically you need to confine them to a room like a bathroom, or a large cage with only food, water, bedding and the litterbox. As they begins to use the litterbox consistantly you can expand their space. There is more information at this link:
link
You need to thoroughly deodorize wherever the cats have been peeing and pooping. Petastic is highly recommended as is Heavens Own. It is the smell of the "accidents" that causes a cat to reuse the place and even if the cat pooped because he was afraid of the thunderstorm, he may be returning to that spot because he can still smell something.

Check into using Feliway, a spray that mimics the happy scent cats leave when they rub their check against something. You can get it from your vet or from Cat Faeries at http://www.catfaeries.com
If you visit the website, you will see a phone number that you can call and for a fee discuss your cat's problems with someone. The person who does this is very knowlegeable and it may be worth the $$ for you. Feliway is also available in most large pet supply stores. There is also a Comfort Zone plug-in with Feliway that can help.

Finally, if all else fails, ask you vet about using an antianxiety medication such as Buspar or Prozac. These very often work, however the decision to prescribe them will rest solely with your veterinarian who will be able to monitor the dosage and side effects.
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Smile, it will make them wonder what you are up to!

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