When Joseph went to the scriptures for clarity and understanding he didn't read a scripture that told him that the true church of Jesus Christ wasn't on the earth. He read a scripture that gave him his next step. And through the power of the Holy Ghost that accompanies the scriptures he was lead to do that which would ultimately give him his answer. They same is true for us. We can receive answers for our confusions, doubts and problems in the scriptures. God, though the power of the Holy Ghost can teach us "all things that we should do."