1) 시험 잘 못 보는 줄 알았어요 = I thought I don't do well on exams (that is, a type of person who doesn't perform well on exams)
2) 시험 잘 못 볼 줄 알았어요 = I thought I would not do well on the exam (e.g., until I did the exam, and afterwards, I changed my mind)
If you mean that you were pleasantly surprised after you got your results, but during all this time, you thought you did badly, you would simply use the past tense, not the conditional as in (2) above.