This can be done in BES 4.0 but it had HUGE bugs. I think they are mostly fixed with 4.1.6. But also you can crete the custom IT Policy but you need to create the software on the handheld to use the ITPolicys that you create on the BES.
You cant just create some Random IT Policy and want it to work with the hanheld, unless you create the software for the IT Policy on the handheld. Then it will work. Does that make any sence?