Hey Rhino;
If you do have some really "rotten pieces" (give them the sniff test, phew!) see if you can locate the source of the smell and scub it off with a toothbrush. It's more than likely a dead sponge and can either be black or whitish in color; it's also likey to be slimy, blech. You want to trigger the cycle but no use having that much dead stuff in the tank
I saw very high ammonia the first week, 10 days my tank was cycling, then the nitrites and nitrates start to show up. You can do small, frequent water changes during cycling to help keep the levels down. You may not complete the cycle quite as quick but you may keep more of the life on your rock by doing water changes.
The next thing you'll probably see will be an outbreak of diatoms, a brown dusting over the glass, rocks and substrate. It's normal but looks likes heck so don't panic. This can last for a few days to a few weeks, you can never tell, but small water changes and lots of circulation will help. Diatoms feed on silicates so it's important that you use a good water source for top off and for mixing your salt water for changes.
HTH and enjoy!
~Alice