Do you have a reference for the process of setting the fuses through IDE or is it best to do another proceedure for setting the fuses? (say AVR Studio)
I don't know about the IDE, I have always used AVR Studio 4. When you invoke the programmer there are several tabs. Select the 'Fuses' Tab and then put your Hex values in using the lower section of the window.
Be absolutely sure that you put the correct value in the correct place. If you get them mixed up you can make your chip appear bricked requiring the use of programming techniques not provided by the AVR ISP to undo. Don't ask how I know this.
Why are the settings different from the Mini to the Pro mini?
I am not familiar with either.
Don