To see what being passed to 'cob', simply set the 'verbose' flag in the Project Properties page. You will then see the various options that are passed when a build is done.
At the same time, you'll probably want to also enable the 'Generate Directives File' as that contains additional directives that we pass to cob (it will be created in the New_Configuration.bin output directory)
Compilation of a project is handled by a standard Apache Ant script. This is generated from the project and is located a tthe top level of your project called .cobolBuild. This file can be run under Ant if you so desire.
There are dedicated Ant tasks to handle the COBOL compilation so you won't be able to see exactly what is passed to cob though from here.