Since you only have one source, the ICBM could go either between the SACD player and the pre-amp or between pre-amp and amp, but if you put it between pre-amp and amp then the sub volume will track the main volume (since the ICBM is downstream of the pre-amp's volume control).

I'm not familiar enough with the PT5 to know exactly what it does on the high pass, full range, and sub outputs, but I can offer some thoughts on what the ICBM would do for you. The benefit of the ICBM over the PT5 probably lies in two areas: adjustable crossover point (so you can tweak the crossover to best match your Monitor Audio speakers), and the ability to have stereo subs (so that the low frequency from the left channel is routed to the left sub and from the right channel is routed to the right sub). You could connect the full range outputs of the PT5 to the left and right inputs of the ICBM, then go to the amp and go from the left and right sub outputs to the two LFM-2's.