You can (at the moment) not use InnerBlocks more than once within a block. However, you can bypass this by using a template for your InnerBlocks that contain Blocks which support InnerBlocks instead, like the core/column block.
Like this:
wp.element.createElement(InnerBlocks, {
template: [['core/column',{},[['core/paragraph',{'placeholder':'Inhalt linke Spalte'}]]],['core/column',{},[['core/paragraph',{'placeholder':'Inhalt rechte Spalte'}]]]],
templateLock: "all",
allowedBlocks: ['core/column']});
Some time ago, i wrote a Block for a content/sidebar block with align left/right attributes, worked exactly like that.
Happy Coding!