There are 68 collapsible 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.
For example: The logo element is injected into the header-a position. It is inserted in a stacked fashion, meaning, if there are modules published to the header-a position, they will appear in the same column as the logo, just one place below.
You can change the positions of these elements at Extensions → Template Manager → rt_crystalline_j15
The below diagram is of the Module Variations page.