Much of an Academica Pro site is built with widgets — the homepage content, the sidebars, and the footer are all widget areas. Manage them in Appearance → Widgets.
Widget areas
Homepage:
Homepage: Content Widgets — the content column of the homepage templates.
Homepage (Below the Slider) 1/3 / 2/3 / 3/3 Column — the three columns under the slideshow; made for the WPZOOM: Image Box widget.
Site-wide:
Sidebar: Left Column and Sidebar: Right Column — the two sidebar columns; which ones appear depends on the page template (No Left Sidebar / No Right Sidebar hide one).