Welcome to the wonderful world of planted tanks! Let's get started:
1. Sounds like a reactor, depending on the bio balls. Are they the same as what are used for wet/dry sumps, or is it more fluidized like Purigen? Could be a reactor, but could be a fluidized bed filter as well.
2. Depends. Glass tops lower the evaporation rate and prevent jumpers like hatchet fish from getting out, but they block a good portion (10%+) of the light from your Fuge Ray. Your call.
3. I would suggest Miracle Gro Organic Potting Soil (MGOPM) with a cap of medium-grit pool filter sand (PFS) from a pool supply store, or sand-blasting grit from your hardware store. Wash both sand and MGOPM, remove floating organic debris from the MGOPM. Pack some PFS into the edges of the bottom of your tank, fill the center with 1.5" of MGOPM, top with PFS. This is called a Walstad dirted tank.
To start, I would buy some egg crate (a.k.a. light diffuser grating) and cut pieces to use under the substrate to help provide a slope from the back down to the front of the tank, which is advantageous in providing a visual "depth of field" to make your tank look bigger. Add your hardscape in. Do the substrate as stated above. Fill tank half way, plant your plants, set up hardware, top tank off, run tank and change water till the dust from the substrate/planting settles. Add fish & a bottle of ATM Colony or Tetra SafeStart if desired.
Some aquascaping tips - Smaller-leafed plants make your tank look bigger. Dwarf hairgrass is a great foreground plant. Blyxa Japonica, Anubias Nana, and mosses are nice mid-ground, and in the back plants like Rotala Macrandra "green" would be great. Get some trimming tools like scissors and tweezers and read up on how to trim your plants.
That's my advice. Hope it helps!
