Hold all "millis()" values in an array?
This is a classic example where you want to create a class.  A class will contain all the control logic for dealing with one pin - all the functions, all the variables, etc.

Then you just create as many instances of the class as you need for your different pins. Each one is completely separate from the other, and each one can be controlled at will.

For instance, you might make something like this (untested):

class FaderPin {

    private:
        uint32_t timestamp;
        int motor_pin;
        int fadeInterval;
        int minPWM;
        int maxPWM;
        int fadeDirection;
        int fadeValue;

    public:
        FaderPin(int pin, int minp, int maxp, int interval) {
            motor_pin = pin;
            minPWM = minp;
            maxPWM = maxp;
            fadeInterval = interval;
            fadeDirection = 1;
            fadeValue = minp;
            timestamp = millis();
        }

        void fade() {
            uint32_t thisMillis = millis();
            if (thisMillis - timestamp &gt;= fadeInterval) {
                // yup, it's time!
                if (fadeDirection == 1) {
                    fadeValue = fadeValue + fadeIncrement;
                    if (fadeValue &gt;= maxPWM) {
                        // At max, limit and change direction
                        fadeValue = maxPWM;
                        fadeDirection = 0;
                    }
                } else {
                    //if we aren't going up, we're going down
                    fadeValue = fadeValue - fadeIncrement;
                    if (fadeValue &lt;= minPWM) {
                        // At min, limit and change direction
                        fadeValue = minPWM;
                        fadeDirection = 1;
                    }
               }
               // Only need to update when it changes
               analogWrite(motor_pin, fadeValue);
               // reset millis for the next iteration (fade timer only)
               timestamp = thisMillis;
           }
       }

};


Then you can:

FadePin motorOne(5, 0, 255, 10);
FadePin motorTwo(6, 0, 255, 10);


And regularly call:

motorOne.fade();
motorTwo.fade();