For flex fuels to work you need modular fuel tanks installed. You don't need real fuels. When you're in the VAB or SPH go into the action group editor and click on the fuel tank. This will allow you to select any combination of liquid fuel, oxidiser, mono-propellant or Xenon. Pro-tip: You can automatically get the right split of liquid fuel and oxidiser by attaching a rocket engine. What flex fuels also does is allow you to change the texture of the tank to whatever you want. So instead of having loads of tanks you can just have one of each size. It doesn't delete or overwrite anything, so you can always modify the MM config to get back parts you want if they are missing.