As a general rule, you should allow at least 48 hours for each muscle group to recover from weight training. Exercising different muscles on different days is one way to work around this schedule, but a study published in the Journal of Strength and Conditioning Research suggests super sets might require a different approach.
Twenty-five physically active men performed 5 sets of 8 to 10 reps max on 4 different exercises: 2 targeting the legs and 2 for the shoulders. Some did super sets while other subjects separated these exercises. Super sets generated higher muscle activity as well as markers of muscle damage. Researchers concluded that 5 days was not enough time for complete muscle recovery.