I don't think that the large/no sub and small/sub is an issue with the ICBM.

Set all your speakers to large. As I understand it, there will be no output from your receiver to the ICBM sub input via the RCA connection for the LFE/sub channel. However, you will have a connection from the ICBM LFE/sub RCA output to your sub. The ICBM will extract ALL bass, including the bass sent to the mains, center, surrounds, and LFE info (which has been re-routed to the mains), and send it to the sub, in accordance with your ICBM crossover choices.

I haven't thought this all the way thru, but I suspect that the drawback to this arrangement would be that the LFE mix control on the front of the ICBM would not work, since you have no signal coming directly from the receiver's sub output to the ICBM.

I don't think that you would find this to be either a problem or inconvenience.

Good luck!