Hello jnbrex! Welcome to the world of freshwater
Sound's like you've got a lot of questions and I will answer what I can to the best of my knowledge. My explanations are brief, but feel free to ask me to elaborate on anything.
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I would like advice for substrate, plants/no plants, fish stocking, etc
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In the area of substrate I have experience with gravel, flourite, and now recently sand. Of the three I can tell you that I have had success with both gravel and flourite. I will not comment on sand much as I have only had sand for 2 weeks now, but I will touch on it later. Detritus is an issue, perhaps more so in a saltwater tank, it is less of an issue in a well planted tank since the biological material is "recycled" as plant "food". Flourite is a nutrient rich substrate that helps feed the roots of live plants. To be honest, you can grow plants in either. But the books will tell you to layer your substrate with sand on the bottom, a thin layer of nutrient substrate like flourite, and then top with small gravel (pea sized). I would suggest a minimum depth of 3 inches of substrate. Some plants have deep roots and my 2" substrate is challenging to plant in. In my experience with sand, it is an attractive medium, but I would use sand only with nothing beneath it. The downsides to sand are that it will sift to the bottom of the substrate over time if larger gravel lies beneath it. AND that it compacts. However compaction can be treated with a healthy dose of MTS (malaysian trumpet snails). It really comes down to personal preference or aesthetics.
Plants. It is my personal opinion, but I believe that live plants add to a freshwater tank something incredible that cannot be seen in other aquatic setups. It provides a more natural habitat for fish and encourages real interaction with their environment that is natural and gives confidence to the fish. It is extra work and money, but I find the reward to be well worth the costs. Keep in mind, a proper bulb is needed, lighting does not need to be as intense as many suggest. I currently have 15 watts over 10 gallons and have healthy plants. Some succeed very well with plants in even less light. Balance is the word to remember and there is a 4 part article in the live plants part of the freshwater forum. It will answer many questions for you.
Fish stocking IMO is really up to the owner. But the fish should be compatible with each other and given space and retreats. Even peaceful fish can put up a fin to fight if pushed to do so. I've seen neons give in to their piranha bloodline and danios become bullies. But the best advice I have on stocking is to work within what you're given. If the water is 6.8 pH then find some acidic loving fish. It is not difficult to change the pH, but it IS to maintain a changed pH. And the results can be tragic when failures occur. There are natural ways to change the pH that are more acceptable - things like driftwood.
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Is the cycling different from that of a reef in terms of length?
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cycling for my tanks has typically been 2 - 4 weeks for the nitrite to drop and nitrates to show, but pH did not stabilize well until the second or third month.
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How many fish should be added?
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They should be added slowly. Size plays a role, with a general rule of 1 inch per gallon. But given the conditions and parameters of the tank as well as fish type, there can be more or less fish. For example, in my 10 gallon i have 7 zebra danios. As danios grow to 2 inches in length, by the rule I should only be able to house 5. However i have quite a stock of plants, good filtration, and consistent maintenance. I could support more, but territorial and space issues begin to limit/strain the inhabitants.
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He wants small schooling fish
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I have had neon tetras, cardinal tetras, rosy barbs (mine stayed in a group together), and currently zebra danios. These are only a few of many small size schooling species. But like I said, let the local water supply dictate your range of inhabitants.
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What should the fish be fed with?
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I feed my fish primarily flake (ground up in fingers for small fish) or hikari small fish pellets (they look like colorful grains of sea salt) and my betta gets occasional freeze dried plankton snacks.
What kind of filtration should be used?
I use HOB (hang on the back) filters, had one on my 29 gallon. I currently use one on my 10 gallon and nothing on my 2.5g. Plants help manage fish waste, but you can only do mechanical filtration. Carbon must be removed to allow nutrients to stay in the water for the plants. I have heard good things about sponge filters, but have not used one. As long as weekly water changes are carried out, then the bio-wheel should be good. The sponge should supplement the surface area for biological filtration that is lacking in the biowheel.
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What should the nitrate and pH be?
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Nitrates should stay below 40ppm. I typically get results around 20ppm because of plants in the tank. A pH of 7 allows the most diversity, but it is best NOT to augment the source of water being used, in my opinion.
A sump is not necessary for a freshwater tank.