[[1) Would fertilizers harm the toads? This includes Flourish Excel, an organic carbon source.]]
Avoid fertilizers. Some of them are harmful to FBTs, but I don't know which ones. It's better to be safe than sorry, so just skip the fertilizers. They aren't really necessary for plant growth anyway.
[[2) Would a small gravel substrate (eco-complete) be alright?]]
Again, avoid small gravel. It can be ingested by your FBTs, which can then cause an impaction. Try to use smooth river stones. They're about the size of a thumb and look very natural.
[[3) Do FBTs prefer calm water or flowing water? How deep can the water be without being dangerous for the toads? ]]
They prefer calm water. If you have a filter, point it at one of your walls to create less water movement. The water can be as deep as five inches for breeding purposes, but for general maintenance two or three inches of water is fine.
[[4) Could FBTs live peacefully with small fish, such as white cloud minnows?]]
Fish are really, really dirty. Their oils could be harmful to your FBTs, and your FBT's skin toxins could be harmful to them. Plus, they'll cause stress to your FBTs. Keep your tank FBT-only and you shouldn't run into too many problems.
Best of luck with everything!
Thomas