Hearthstone doesn`t need to be on top of other windows, it just needs to be in windowed mode (not fullscreen) for the bot to work.
Make sure Hearthstone is running in windowed mode (NOT minimized) and it should work fine :-)
You can still use other applications (Chrome...) on top of Hearthstone, just keep it open and don`t minimize it (you can minimize HearthRanger though).
Set it up through the in-game options in Hearthstone or press ALT/Enter to quit fullscreen.