Hi there,
To answer your questions:
1) Ammonia comes from the fish as waste products.
2) Yes and it is pretty straightforward.
If you intend to do some planting in the substrate, then it will take awhile. Do the following steps:
a) Drain out some water into a separate pail, remove your existing plants.
b) Catch all your livestock and place them into the pail
c) Run your existing filter off the pail that contains your livestock. It is vital that the filter constantly has a flow of water in it or else disaster may follow.
d) Do what you have to do with the aquascaping part.
As for part D, if you intend to do planting in the substrate itself, you will need to purchase base fertiliser, bacterial cultures to seed the substrate and the necessary substrate of which you have to choose between several options. If you don't want to do this since you're aiming for a low tech scape then just go with a thin layer of lapis sand. I have a tank with a layer of GEX Mutsu sand which is very nice to look at. This is a very good article on what to do for a typical planted tank:
http://www.gcshop-sg.com/learn_v.php?aid=21&topic=2
However, if you want to skip all that and do the scaping right there right then with your fish still in the tank. It is very simple. Just get a small pack of sand, preferably one that isn't so dusty to look at. Any fine particles in the bag can cause problems for your filter. This is what I do if I want to do a quick scape with no substrate planting:
1) empty a bag of sand into a plastic tub (thoroughly washed)
2) rinse the sand until it is clean with tap water.
3) once the sand is clean, i just scoop it up into a "tau huey" tub and slowly lower it into the tank
4) pour out the sand slowly and it will land on the bottom easily
Or you can skip all that and follow this video on Youtube that I found awhile back:
Extremely simple method just need some patience and practice.
If you pick the thin layer of sand method, after placing the sand in place, just get some Anubias or moss or Java Ferns on driftwood and scatter them all over the tank. Arrange as you wish and the fish won't be bothered one bit. Just make sure you rinse the plants and the wood well because some plant farms do use pesticides on plants grown emersed like the ones I mentioned. Any trace residue can have adverse effects on your fish.
After the scaping has been done, turn off the lights to let your fish calm down. For most part if you do this slowly, they won't be overly stressed and you won't have to get pails and what not.
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