struct MuxRegister {
Uint16 PIN1:2;
Uint16 PIN2:2;
...
}

#define LED PIN1      (in a different file of course)
#define PWM      PIN2
#define Mux_GPIO 1         (value from 0-3 selects different options)
#define Mux_PWM  3
MuxRegister.LED = Mux_GPIO;
MuxRegister.PWM = Mux_PWM;
...

#define BIT1 0x00000001
#define BIT2 0x00000002
#define BIT1 0x00000004
#define BIT2 0x00000008
#define LED (BIT1&&BIT2)
#define PWM (BIT3&&BIT4)
MuxRegister |= ((Mux_GPIO && LED) || (Mux_PWM && PWM) || ... ;