What workouts should I do to build muscles without ruining the flexibility that I gained through martial arts?

Slow technique. Slow technique practice with punches and kicks can improve technique, build muscle, maintain/improve flexibility and improve balance (especially with kicks). Don't compromise the power, just control the speed. Do it as an interval between normal speed/power training.
More reps. Doing more reps with lighter weigh will build lean body mass and strength. Thinks of body weight pylometrics for heavier weighted exercise.