Summarizing Qin family's current family chart for anyone who is confused (based on the drama as of episode 16):
Qin family has 3 branches based on the 3 sons from the second generation: Qin Shu (first branch), Qin Liang (second branch), and Qin An (third branch).
***First generation:
Grandfather Qin was the former Marquis of Zhongyong and he has already passed away.
Grandfather Qin had a legitimate wife (who also passed away already) who birthed 2 sons; Qin Shu and Qin Liang.
The current Madam Qin who is in control of the household in the Qin family ancestral home is the second wife of Grandfather Qin. She birthed Qin An.
***Second generation:
1) First son: Qin Shu. Current Marquis of Zhongyong, in the palace currently, and regarded highly by the crown prince. Qin Yan and Qin Zhaoyu are his legitimate children.
2) Second son: Qin Liang (the one who saved Shen Wan in the beginning). He is not close to the family and left to live in the Medicine King Valley years ago. His wife also passed away years ago and his daughter is Qin Wan (passed away a year ago at the start of the story).
3) Third son: Qin An (the man playing with the crickets in episode 1). Qin An's legitimate wife is Qin Lin (she is weak-willed and is seen hanging around Madam Qin a lot) and they birthed 2 children: Qin Chen and Qin Xiang. Qin An also has concubines and has children with them. His current favorite is concubine Liu. He used to have a concubine named Yang.
***Third generation:
1st Young Master: Qin Chen (ambitious and very different from his dad or so he thought). His legitimate wife is Xinlan and she ends up giving birth to a girl. Legitimate son of Qin An.
2nd Young Master: Qin Li (the one who has syphilis). Son of Qin An and one of his concubines.
3rd Young Master: Qin Yan. Eldest son of Qin Shu/current Marquis of Zhongyong.
5th Lady: Qin Xiang (Madam Qin's favorite granddaughter). Mrs. Huo wanted her to marry Huo Ning instead of Qin Wan. Legitimate daughter of Qin An.
6th Lady: Qin Shuang (the one who got canned for talking shit about the Grand Princess and who Qin Wan saved from the well). Daughter of Qin An and one of his concubines.
8th Young Lady: Qin Zhaoyu. Oldest daughter of Qin Shu/current Marquis of Zhongyong. Candidate for the Crown Princess.
9th Lady: Qin Wan (our girl). Had an engagement with Huo Ning. Later adopted by the Yue family per Yan Chi's suggestion.
4th and 7th of this third generation are currently unknown.
