All controls at left including the command interface (at bottom) can operate on either molecule simply by selecting Top or Bottom (upper left). Mouse-driven rotations or zooms can be synchronized between the two molecules (one follows the other; not available on Macintosh).
All control panels in Explorer are available in Comparator (title is replaced by top/bottom selector).
The snapshot below shows the QuickViews control panel.
(The links in the snapshot don't work since this is just a snapshot.)