Hi...when it says to stop filtering while treating with medicine, it means to remove the carbon from your filter. Keep your airpumps running, just remove the carbon during the treatment so the carbon won't pull the med out of the water. But when you're done with the med treatments, use your carbon to remove the last traces of the med. This is how I use carbon -- just to remove medicine. I don't run it in my tank every day. I just have a very small corner filter to use with my carbon. It takes about 24 hours to remove the med. Your filter sounds like it's much more powerful, so it may only take a few hours for your filter and carbon to remove the med.
It's good that you are changing 75% of the water if your ammonia is that high. Here is a good website to explain cycling:
http://www.aquamaniacs.net/cyclingsafely.html There are tons of cycling info on the web, but this is a site that I like and have referred to a lot. You'll have to keep doing frequent water changes, probably every day, depending on what your ammonia reading is, during the cycle. But hopefully you won't have to do another 75% change! You should get an ammonia test kit, a nitrite test kit, and a nitrate test kit to see how your cycling is coming along. You'll have to do water changes to keep the ammonia and nitrite levels down. When the ammonia and nitrites are 0 and the nitrates are 20-40
ppm, your tank has cycled, and the water changes every day will end! Then you do water changes to keep the nitrates from getting higher than 40
ppm. You may only need to do this change every few weeks. Use your nitrate test results to tell you when to make this change.
I would not add things like am-quel or ammo-lock to lower the ammonia. Just do your water changes. Adding the am-quel or ammo-lock seems like a fast and easy way to lower the ammonia, but these products, if added heavily and frequently, may interfere with the cycle that you're trying to start. The article I suggested says you can add a one-time dose of am-quel, 10 drops a gallon. I use this dose when I'm making up my tap water, but I don't add any more after that. I would just rely on frequent water changes to lower the ammonia, and when the cycle is completed, then your water changes won't be as frequent. Hope this helped!
p.s. Here is a good article on ick too:
http://www.aquamaniacs.net/ich.html