So when you cycle your tank, it goes through ammonia, which comes off your live rock, or dry rock that has dead stuff on it. Then turns into nitrites, then nitrates. Your best to let it al lcycle together and create the right bioload for your first fish.
I would just leave the rubble in the sump and the LR in the DT. It will all become live rock one way or the other.
Just let it run, when your ammonia is 0 in the tank and your nitrites are 0 and your nitrates are whatever number, start doign water changes and your good for fish. It will make no difference to the cycle with the dry rock in there. and the smell will go away.