If you are doing straight lines, i don't see the issue, try rotating your view a bit, or where you are standing to get it to line up. You also may need to build temporary stair cases to get you in the right place. Roofs are a bit annoying, but stick some wood on top of stone, then click the roof onto the wood. Use the square stuff as well, logs are fine but the way roofs click to logs is painful. Good luck.