Hi, My son is currently at Plovdiv Medical University. He's currently going into third year so I have a bit of knowledge about the application. We originally tried applying direct but found it a bit challenging so resulted with an agency.
The application process is somewhat long; but hey it is for medicine! The best thing I found was the comfort of having things done and the hastle taken of our heads; especially when we flew over (trust me its not as easy communicating in bulgarian as some may think), they were helpful in arranging all the things necessary for us to move and settle in as well get the feel of the environment. They introduced us to all the relevant people and showed us all the places my son could find useful. This all helped ease our nerves actually allowed me to feel comfortable leaving my son there after a week.
All I would say is, in my experience applying through an agency is beneficial as it gives you the support one needs when one is in new country.
Hope this helps.