How to crop original source w/o skewing aspect ratio?

Hi, I am using wowza with Amazon EC2 (MarketPlace AMI)

I tried to crop incoming vertical movie (with size 720 x 1280) into 720 x 405 using transcoder.

but I can’t grasp the rules of cropping. The engine manager requires the number of pixels from the edge, but when I all form filled with zero, it seems that the original movie will be cropped from the center. In addition, when I fill the form of bottom with 400 - 500, it will be cropped but with skewed aspect ratio.

May I ask someone to tell the rules of cropping?
- how to specify the area of cropping
- when cropped movies skewed, what can be the causes?