A Protocol is any notebook Entry that has the word "protocol" in its title. Protocols are special because you can inject a copy of a protocol's content directly into another entry. You can view all the lab's protocols in the 'Protocols' link in the side menu.
Inserting Protocols into Entries
In the Entry type a plus character (+) at the beginning of a new line in your entry. Keep typing to filter the list and simply click one in the list to copy its content.