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Even though you moved some gravel and a filter from the old tank you will still need to go through a cycling process. The process should take a shorter time with the things from the other tank. This is why you are getting ammonia now because of you starting a new cycle Also like you said, the rinsing of filter media in tap water killed some of your bacteria. Adding the Prime is good. It will detoxify the ammonia. But to keep the ammonia levels down you need to do water changes since you are cycling with fish. I haven't cycled with fish in so long I forget how often you should do water changes. I would do frequent changes of 30 or 40% to keep the ammonia levels down.

For your filter, in my tanks I try to have 10x turnover rate of the tank, so in a 46g I would try to get 460gph. I tend to over filter and 10x really isn't needed, it's just piece of mind for me. At a total of 300gph (empty without media) the penguins should be ok if you really keep up on your weekly water changes and don't over stock the tank.

For the heater, I use a 150w heater in my 55g without any problems. Ideally you want the lowest wattage possible so if it breaks and gets stuck on it won't boil your fish.

For the tests, most use API which are sold and any LFS or petsmart etc..
 

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I would also read this http://www.cichlid-forum.com/articles/cycling.php to keep you updated on the cycling process and what to expect through out. But again, since you are cycling with fish, frequent water changes (don't forget to use the prime) will be needed to keep your fish from dying.
 
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