PeterH has the right idea. One nicety would be to have the two target values achieved at approximately the same time.
To do this, you could decide how long, in millis() you want the total dimming or brightening to take place, then divide that time (integer divide) by the number of steps it requires for each strip. You then set a duration variable for each strip, containing the length of time required for one change in value. Eqch time the duration for each strip is passed, you increment or decrement the value of the PWM, until it reaches the target value (or passes it),