Your tank should be up and running with everything running as if you had fish in it when you cycle your tank. Once your tank is cycled you should be fine, you shouldn't have to cycle your tank again.
When you cycle your tank your letting the good bacteria build up on the live rock and sponges of your filter. You should never replace a sponge in your filter unless it's about to disintegrate, at which point you just put another sponge in in front for a few weeks to let the new sponge get seeded by the old. Your carbon filter is fine for keeping the water clean, but you need some kind of sponge for your good Bactria to cling on too. that is behind your carbon filter. Only the carbon filter should be replaced every few weeks. You clean the sponge with old tank water, just a quick swish in the bucket of old tank water you took out of the tank that day to do a PWC
. Never squeeze the sponge out, just enough swishing to get the big stuff off. Than put back into your filter.
Again when it comes to cycling your tank, you are letting the ammonia build up, which in turn turns into nitrites and than nitrates. You want 0 ammonia and 0 nitrites. Once your test read that (Should take 3 to 6 weeks), do a 90% water change and add back your Clowns. The good Bactria is in the rocks and sand and filter, so the water change is not going to effect the Bactria colonies.
The only reason I said to use the stocking is because the shrimp is going to get nasty. I didn't use the stocking and I nearly puked when I pulled it out with my hands. :-p Also if you have anything in the tank that is alive they might die. So good luck, cycling the tank is never fun, but once it's cycled it will save you a lot of money and fishes lives. Oh and while the tank is cycling, don't do water changes!
What do you mean again in the same tank? Once the tank is cycled the Bactria colonies should be stable unless you do something. You could add too much fish at once and shock the bio-load and it will do a mini cycle, but once you cycle the tank it should be cycled. Just go slow and add fish in slowly!! Once you have it cycled, 2 Clowns should be fine. My first fish were 2 clowns and nothing spiked for me. You should wait at least 2 weeks after before putting any more fish in!! Every fish you put into your tank, you want to wait at least a week to add another so the good Bactria can catch up.
Just make sure any fish you buy you do your research on before putting into your 29 gallon tank. I have a 29 gallon tank and only have 4 fish in it, not a lot!! You can do maybe more depending on the fish you get, but not much more.
I did this only once and what I told you is my experience! I hope more people chip in and help. I have had good results and no fish death due to poor water conditions. I had one jump out. :-/ Only death I had. Other than that, 2 and half months and no issues.