Active LEDs are chosen like --LED 1001101010 (more than one is possible at the same time, although maybe not recomended). Several mDOMs can be placed, and one of them should be used as emitter with --emitter_mdom.
IceColumn properties and position can be tunned with input parameters, although for some of them the visualization might not work.
One can set no ice properties for the bulk ice with --bulk_ice 0 and therefore there would be scattering and absorption only for hole ice.