They should be stored pointy end down. For best results slant or turn the eggs 30-45 degrees daily while storing (you can tilt the eggs by putting something under one end of your carton and then switching it to the other side every day). Also, a temp of about 55°- 60°F and 70-75% humidity is ideal for storing eggs. Make sure to allow them to warm to room temp before you put them in the incubator though. Oh, and
They should be just fine if you've been storing them on their sides. The main reason people suggest storing them with the pointy end down, is because they're harder to break that way. Storing them on their sides will not affect your hatch rate, so unless you want to start over for some other reason, the eggs you have should be fine.