In the line-breeding program you start by breeding your best cock to your best hen. If you are going with the cock line, you will breed him to his best daughter, then his best granddaughter, and then to his great-granddaughter. I like to wait until the hens are at least 18 month of age before I breed them, even in a line-breeding program.
If you are doing a Maintenance program (spiral / rotational system), you will always keep the hens in the group they came from. All hens in group/pen A, stay in A. You are only going to move the cocks to the next group. Always move your best cock! That my be the original cock, or it could be his son, which ever one is best.
I would always hold onto extra stags and cocks, especially if they show potential. You never know when you will lose a bird.
Does this answer your question? If not, let me know and I will clarify more.
Remember, we can always do a coaching call if need be. I record these calls so you will have a copy, and I use them for future podcast for helping other members.