If you're following an upper body intensive program that is primarily bodyweight, we don't recommend combining weight lifting. With our retired skills programs (p1, f1, r1, p2, f2, r2), because of the level of intensity, adding in weight lifting would likely result in overtraining.
However, when it comes to training your lower body, that's where lifts like squats and deadlifts fit in perfectly. Some people prefer these movements over bodyweight exercises for their legs, and they work well with our programs. We recommend training your legs on an off day as a separate session to ensure your body feels fresh and you don't overwork yourself.