If I have allergies, how can I ensure proper nutrition?

Depends. Assuming you are talking about food allergies (you didn't specify), the best course of action is: figure out what your allergies are, eliminate them from your diet, enlist a nutritionist and your doctor to work together (e.g. If can't drink milk--get calcium chews and vitamin d, if you can't have wheat, use quinoa and supplement with b vitamins, etc).
Complete nutrition. Despite having allergies (assuming food allergies), it is still possible to obtain full nutrition from other sources. Meats and poultry are much less likely to cause allergies and are a good source of protein. Fruits and vegetables with some exceptions are also less likely to cause allergies and are sources of vitamins and minerals. Supplements also help. Just maneuver around allergic foods.