toolbox.js is the text menu of categories down the side on advanced Blockly apps. flyout.js is the graphical list of blocks down the side on simple Blockly apps, as well as the temporarily visible graphical list of blocks that appears when a category is clicked in an advanced Blockly app.
If you are looking to change the location of the menu on a simple app (such as
https://blockly-demo.appspot.com/static/demos/fixed/index.html), then you can ignore toolbox.js completely (since there are no categories) and try to hack flyout.js to give you a different orientation.
If you are looking to change the location of the menu on an advanced app (such as
https://blockly-demo.appspot.com/static/demos/toolbox/index.html), then you will have to modify flyout.js (as above), as well as toolbox.js. Toolbox is a wrapper for Closure's TreeControl, which forms the display. Attempting to reorient TreeControl could be an adventure.