Marek's and Cocci vaccinations ae totally different things.  They are not related.  If you get the cocci vaccination, do not feed the medicated feed.  If you get the Marek's vaccination, it does not matter if you feed the medicated feed, unless you also get the cocci vaccination, of course.  
The vaccine they use for Marek's is Turkey Marek's.  It does not prevent chickens from getting chicken Marek's but it does prevent the lesions that chicken Marek's causes.  The lesions are what causes the problems.  Chickens that have been vaccinated with turkey Marek's can still get chicken Marek's and can give chicken Marek's to other chickens.  Vaccinating them with Turkey Marek's does not mean that they have chicken Marek's but it means you don't know if they have chicken Marek's or not.  
There are seven different protazoa that can cause Coccidiosis.  If a chick gets immunity against one, it does not automatically have immunity against the other six.  The vaccination that McMurray was using last year protected against three of the seven.  I don't know what they are using this year.  For the chick to develop immunity after the vaccination, it has to go through a few cycles of the protazoa reproducing in its intestines, the eggs coming out with the poop, the eggs developing in slightly moist poop for a day or two, then going back through the chicks system when it eats some of its poop.  If you feed medicated feed or give the chick antibiotics while it is developing this immunity you negate the effects of the vaccination.  I believe it  takes two weeks of this cycling before the chick develops the immunity.
Different "organic" certifying organizations have different rules and requirements.  If you are planning on becoming certified organic, i suggest you talk to the organization that will certify you and see what their specific rules are.  I don't know about vaccinations specifically buit at least some certifying organizations do not consider feed medicated with Amprolium to be a problem with certification.  Amprolium is not an antibiotic.  Amprolium is often the "medicated" in medicated feed.