The cycle that you're referring to is the establishment of a sufficient population of nitrifying bacteria that will process the byproduct (ammonia) of the decomposition of organic matter so more complex organisms can live in a safe environment.
The process happens naturally so there is very little you can do to prevent it.
Test your ammonia, test your nitrite. That will tell you what stage the cycle is at. Both should be at zero.
Scrubbing and rinsing the live rock will help wash away organic matter that still needs to decompose, that will help your nitrifying bacteria population will establish itself faster.
The smell you're detecting is the result of recently disturbed decaying organic matter, most likely hydrogen sulfide.
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Mitch
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