Any shipping module that uses weight for the calculations also takes into account a built-in Tare weight.
The Tare setting (configurable in your store Admin) adds extra weight to compensate for packaging materials.
To change the Tare point your cursor at the Configuration menu, choose Shipping/Packaging from the menu and change the Tare.
You can set either and/or both a percentage or weight for Tare and Large Package.
Entered as percentage:weight
Disabled completely = 0:0
10% + 1lb = 10:1
0% +3lb = 0:3
5% + 0lbs = 5:0
This way both the Tare for small to medium packages has a flexible option of percentage + weight and the Large Package increase has an option of a percentage + weight.