I know that we are not meant to use herbals or vitamins when on the protocol but can we still cook with spices?

Cooking with spices is fine. Its just that we cannot always trust what is contained in the capsules and tablets sold as a nutritional supplement. In addition, the amount of herbs and spices given in the form of a supplement are much larger than what are commonly used for cooking. As an example, the spike in blood levels of vitamin C when taken as a supplement are much higher and may have different cellular effect than small amounts of vitamin C that trickles into our blood stream as it is absorbed from the foods we eat.