It's really simple :).
They are both Beginner sections but they differ in a couple of ways.

1. The Scholastic Section is reserved for students and schools participating in the Magnificent Chess-in-Schools Programme AND all other students from the primary through to the high school level (even if they are not a part of the Mag Chess-in-Schools Programme). The Amateur Section is open to UWI/UTECH students and non-students at the beginner level (rating of 0 - 1299).
2. They take place on different dates. The Scholastic Section takes place on Friday March 20, while the Amateur Section takes place on Sunday March 22.

Please see the schedule at the link below:
http://www.magnificentchess.com/?q=news/most-magnificent-chess-week