First, realize that you will work each of these muscles or modalities alongside or on top of your program. These workouts are actually layered on top of those training sessions. Meaning you complete your program as designed and then follow a Specialization routine simultaneously.
Determine which body part or athletic attribute needs the extra attention. Every athlete has a particular desire they wish to emphasize and the program you are following will begin to mold you into that athlete but this will further enhance that. Do this by taking an honest audit of one muscle or attribute that you severely lack the development of. Choose that attribute that you have experienced is stubborn to grow, mold, or develop.
It is essential that you follow exactly how it is programmed. Do this for 6 - 8 weeks without missing any of the workouts.
Must note that "Specialization" is not meant to chose 4 - 5 different attributes at a time. This would cause too much stress on the body and potentially lead to overtraining. The focus and concentration on one particular attribute for 6 to 8 weeks will yield much better results than trying to develop multiple attributes at once.
After completing one phase of Specialization then move to the next weakness of yours or repeat the same one over again.
Chest
Back
Legs
Shoulders
Arms
Core
Linear Speed
Vertical Jump
Agility