Use Function Keys as Keyboard Shortcut
I think you got two options:


Enable function keys to work like normal keys and to activate their special functions – like increasing volume etc. – when pressing fn beforehand.


Open System Preferences
Select preference pane Keyboard
Select Keyboard tab
Activate option Use all F1, F2, etc, keys as standard function keys



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Set custom app shortcuts for your programs that need function keys in their shortcuts.


Open System Preferences
Select preference pane Keyboard
Select Shortcuts tab 
Select group App Shortcuts
Press + and add your needed shortcuts – those already existent in the editor. Just select the corresponding app, insert the shortcut name (name in the menu connected to the shortcut) and enter shortcut already set by the program.



  Image taken from Geeksays.com