How do I run two Arduino sketches at once?
It would help if you added the current source code. Probably you use delays, in that case, use millis() instead and use the same technique as the Blink Without Delay example.

When using delay, it will cause your program to 'halt' not being able to do actions concurrently. With keeping a state (and time since last state change) for both motors you can check for a time to elapse to do the correct actions for one or both motor.