Autodesk Quantity Takeoff

[#1]

I have Autodesk QTO 2013, Im currently working on a project using PDF files . Poor contractors. My problem is that in the plan and profile sheets the scale is different for each axis. I would like to know if there is any suggestions for this issue. I need to get a little bit more accurate with the qty it seems that i am getting 8% or more at times without having the correct scale setup.

[#2]

Do you need to take off area measurements or linear?  Why the exaggerated scale - are you working with cross sections?