There is not a vaccination available for cocci. If you want to medicate against it, then you can feed a medicated chick starter food.
As far as other vaccinations go, it all depends. Some are administered differently than others. For instance, the Infectious Bronchitis/New Castle vaccine can be given as drops in the eyes or nares, or mixed in with the water. If you go the route of the water, then it's a bit trickier. If you vaccinate for Coryza, then you are going to give a subcutaneous shot at the base of the neck. If you want to vaccinate for Mareks, this needs to be done when the chicks are a day old and in the base of the neck like the Coryza vaccine.
Each vaccine is different, but they do come with instructions and are surprisingly easy to administer.