Based on your score of 54 marks in AP EAPCET and your impressive IPE marks of 560 out of 600, you have a good chance of securing a seat in BSc Agriculture. However, whether you get a free seat depends on the cutoff set by the college or university for this year, the category you belong to, and the availability of seats. Usually, higher IPE marks improve your chances in the counseling process. I recommend checking the official counseling details and participating in the seat allotment rounds to know the exact outcome. Keep an eye on the latest notifications from the admission authorities for updates.