In "verb/adj는 걸 보-니까", 보다 means "to see, look at, watch or experience" and a connective ending "-니까" is used as the conjunction, meant "because" or "for" in English. In "verb/adj (으)ㄴ가/나 보다", 보다 means "to seem, appear, or assume" for example, 그가 갑자기 빨리 뛰는 걸 보니 학교에 늦었나 보다. He seems to be late for he run so fast suddenly. 그런가 보다. It seems be so. 이렇게 늦는 걸 보니, 차가 막혔나 보다. Because he is so late, It seems that there was a traffic jam.

-나 보다 means "I guess/assume...", used with action verbs. -(으)ㄴ가 보다 means "I guess/assume...", used with descriptive verbs.