In general, it is recommended to position eggs in an incubator with the large end up and the small end down. This orientation helps mimic the natural nesting behavior of birds and can improve the likelihood of successful hatching. Here's why:

1. **Air Cell Development**: When eggs are incubated with the large end up, the air cell, which forms at the larger end of the egg, remains at the top where it is supposed to be. The air cell serves as an important point of reference for the developing embryo and helps facilitate the chick's internal positioning for hatching.

2. **Prevention of Embryo Rotation**: Placing the eggs with the small end down helps prevent the embryo from rotating during incubation. Maintaining a consistent orientation throughout incubation can reduce the risk of developmental abnormalities and ensure proper positioning of the chick for hatching.

3. **Minimization of Contamination**: Positioning the eggs with the small end down can help minimize the risk of contamination from any debris or bacteria present in the incubator. By keeping the small end of the egg closer to the incubator tray or rack, it is less likely to come into contact with contaminants that may affect embryo development.

4. **Natural Incubation Behavior**: In nature, birds typically lay their eggs with the large end up and the small end down in the nest. Mimicking this natural orientation in the incubator can help create a favorable environment for embryo development and hatching.

While it is generally recommended to place eggs in the incubator with the large end up and the small end down, some incubator models may have specific instructions or features that dictate a different orientation. Always refer to the manufacturer's guidelines and follow best practices for egg incubation to maximize hatch rates and ensure the health and well-being of the developing embryos.