Final answer:
Organizational challenges and lack of manpower were the main flaws in the Continental Army's formation, while equipment shortages affected its operation.
Step-by-step explanation:
The two main flaws in the way the Continental Army was formed and operated were a significant lack of manpower and ongoing organizational challenges. The army was composed of units from all colonies, each with its own approach to military organization, leading to issues with uniformity and discipline. Additionally, equipment shortages plagued the Continental Army, making it difficult to uniformly equip soldiers and bringing a wide variety of uniforms into the ranks, negatively impacting unity and discipline.