Your best bet is to look at the GUICreate functions in the help file as it's a lot easier to achieve what you want to do. My advice look at GUI management and search for $WS_EX_TOPMOST.
Otherwise you can do it like this, but InputBox is very limited when you want to delve into bigger and better things >>
Local $hWnd = WinGetHandle(AutoItWinGetTitle()) ; Get the handle of AutoIt's hidden window.
WinSetOnTop($hWnd, '', 1) ; Set it ontop.
InputBox('', '', '', '', Default, Default, Default, Default, 0, $hWnd) ; Pass $hWnd to the handle parameter.