Yes - you have to manually edit your binds file (having a "save as" button in settings is too difficult it seems).
There are threads about doing this, the main thing is that the game uses the preset name from within the file, not the file name. So basically you make your changes in the options / controls screen, click apply - that saves the custom.3.0.binds file - now go edit that and change the file name and the Root PresetName in line 2 of the file (if you are using notepad). Now do the same (different name) for your other set of control settings. The game will now show the two different named profiles that you have edited in the drop-down menu - change to your hearts content.
2 things - If you don't have a controller plugged-in that you want to use when you start the game it defaults to a "custom" (I think) and writes the error in a file in the bindings directory. Finally - don't keep copies in the same directory, the game gets confused if you do.
