Lily, I moved your question into the general exercise forum because I think more people will read it here and hopefully be able to help.
A stairstepper is a cardio machine and can be used interchangeably with any other cardio machine in the gym, such as a treadmill, bike, or elliptical. If the stairstepper is giving you problems, yes, most definitely switch off with other kind of cardio. Cardio shouldn't ever hurt -- the goal is to elevate and sustain your heart rate, not cause pain!
As for whether you're overdoing it, cardio almost every day is fine. But weights six days a week is overtraining, if that's what you've been doing. If you're going to alternate upper and lower body workouts, four times a week in plenty. Muscles grow when you're resting, and if you don't give them adequate recovery time between workouts, you're undoing all your hard work in the gym.
And any time a part of your body is screaming in pain, you need to listen. Too many people start out on fire in the gym, overdo it, get hurt, and then have to completely lay off for weeks. For the first weeks and months, don't push as hard as you can and never, ever workout through pain. It takes time for your tendons and ligaments to strengthen to support your new muscles. A shocking number of new gym members get injured in their first four weeks and I don't want you to be one of them!