Greetings Seble,
After you have determined possible hazards and the controls of preventing cross-contamination you will have to check their effectiveness. Examples are evaluation of the cleaning procedures by having swab tests on surfaces and allergen tests (for microbiological and allergen presence respectively) or air testing with a petri dish for TVC/Molds-Yeasts and any other possible environmental hazards you might recognize.
All these you will describe in a documented procedure, where you will have all the hazards, the controls, how and how often you check the effectiveness of these controls, maybe by whom (internally or external lab) etc. You can also include the acceptable limits eg no allergen presence if you handle allergen free products, less than X cfu/cm2 for TVC on surfaces and no presence for pathogens.
These are some examples. What you write in the procedure is easy enough when you have determined all the parameters.
Regards!