in keyboard mode and followed the extended guide on this forum. In this mode ES wont recognise it as a gamepad so I cant configure it in the menu.
That is strange! Because, even if ES configure Input Menu is telling you it hasn't detected a gamepad, pressing a "keyboard" key should get you through the configuration of the controls for player 1 (same as with only a real keyboard connected)! Have you tried pressing a button (mapped as keyboard key), or does the message that no gamepad was found had mislead you to assume that a keyboard cannot be configured via the UI? Going through that should give you a valid retroarch.cfg (as said for player 1), to add player 2 controls you still have to edit the file.