Really depends on your certification scheme, but the basics are these:
1) Identify allergens present in your facility
2) Identify production lines/products that have unlike allergens
3) Conduct a hazard analysis/risk assessment that shows that you have considered all process steps/conditions where allergen cross contamination may occur.
4) Describe your practices to prevent allergen cross contamination
5) Verify that your practices do, in fact prevent allergen cross contamination
6) Describe your allergen storage policy to prevent allergen cross contamination
7) Describe your policy that deals with allergen spills
Basically... we have the following allergens, we have identified areas where cross contamination can occur, these are the mitigation strategies we have put in place to ensure that cross contamination will not occur and these are the things we have done to verify that our mitigation strategies actually work.