painted part, it should be flush with everything else. Also, the gap between that and the trunk lid should be evenly spaced as well. The bottom of the "tonneau" lid should flow perfectly into the bottom line of the trunk lid as well. After talking with RAGTPZ, I was thankful to know what to look for if the storage lid was messed with or misaligned. My top is practically brand new and although they missed a bolt or two, it was perfectly installed otherwise and lines up perfectly. Please post some pics of the car when you get a chance.