While the command line and par file parameters for sample_multi_transcode are very rich, they do not cover all possible things you can configure.
To see cropping in the sample code, look at sample_vpp. The settings to use are in the diagram below. You define the region of interest by the crop on the input/source side, then you place it by the settings on the output/destination side.
This article has more information on the settings used: https://software.intel.com/en-us/articles/scaling-operations-in-intel-media-sdk
sample_vpp.exe -sw 640 -sh 480 -dw 352 -dh 288 -scrX 100 -scrY 100 -scrW 352 -scrH 288 -scc i420 -i test.yuv -o testout.yuv
In the example above, an input file of 640x480 is used. A region with the left corner at 100,100 and a width and height of 352x288 is placed in the output frame of 352x288 with cropX/Y defaulting to 0.
You could add these settings to the VPP init function in pipeline_transcode.cpp. However, what may be even more useful is to put these settings into the transcode tutorial with resize. The tutorials can be downloaded here: https://software.intel.com/en-us/articles/media-sdk-tutorials-for-client-and-server