I took a new nylon brush and removed all the soft stuff that looked like it was already dead BEFORE i put it in the tank. There should be enuf left to die off and get the cycle going with that stuff removed. I added carbon sheets to an area that the water flowed in order to help with the bad smell. Not sure, but some may say that could delay or compromise the cycle, but managing that smell was foremost in my mind at that time.
How's the ammonia looking now? Thru the roof I'll bet.
If its up there already, I'm guessing it'll be OK to remove the rock pc
and do some removal of that excess dead stuff.
One other thing --- no apologizing for not knowing what it takes time to experience. You're doing just fine.