There are 68 module positions. If no module is published to a position, it will not appear, collapsing the entire area.
There are non-standard elements that are injected into the template grid structure when enabled via the template parameter, such as the logo into header-a. These features stack vertically with any modules published to that position.
You can change the positions of these elements at Extensions → Template Manager → rt_modulus_j15
Control all modules positions with Gantry, in terms of widths within the module row, and left/right/middle placement for the mainbody/sidebar area.