I'm not saying this is the right way, I'm just saying this is how I did it.
How to Patch Holes in a Skoolie Floor, Wall, Ceiling, or Roof
Removing the seats left some massive holes in the floor. If left in place, they'd allow water splashing up from the road to get stuck between the vapor barrier under the floor's insulation and the aluminum floor itself. I know it's aluminum, and thus less likely to corrode, but still... it's more important to do it right.
On top of that, I had to remove most of the running and bus lights from Argo, because they were old incandescent bulbs that didn't work and also leaked. This left not just screw-sized holes, but also four inch circle-shaped-holes for the lights that required a metal plate to patch. The bus stop sign also left holes in the wall, which would let water get in there and definitely cause corrosion.
So there were probably almost a hundred different spots that needed to be patched on Argo.

What Material to Use to Patch Holes in Metal?
Some people recommend using JB Weld (a type of two-part epoxy),
epoxy pennies over the holes, and
bondo fiberglass. The general consensus seems that epoxy is the best way to do it, but what about the larger holes like those left from the seats? The epoxy would just drip right down to the undercarriage. So I decided the best way to patch the floor holes, as well as pretty much anything that needs a waterproof seal, is to use fiberglass.
The general idea for fiberglass is to apply epoxy (which consists of a resin, a hardener, and usually a filler) with a brush to the area that needs to be patched, then apply a piece of fiberglass cloth on top of the epoxy, and finally soak the cloth with more epoxy on top. Wait a day, and now you've got a rock solid, structural, and water-proof bond that can easily be sanded and painted.
How to Make Fiberglass with Epoxy
It's best to work in small batches, as the epoxy will begin curing the moment you mix the resin and the hardener. The specifications are written on the back of the hardener; for me, my pot life was about thirty minutes. However, because I'm working in the sweltering heat of a Central Valley summer, that was reduced to about fifteen minutes. This stuff gets hot as it cures.
Put the pump on both the resin and the hardener, and apply three to four pumps of each to your mixing bucket (remember, smaller batches is better, and make sure you use the same number of pumps for the resin and hardener). Using a stir stick, mix this for about a minute, then add colloidal silica in appoximately half-cup increments, mixing as you go, until the mixture has the consistency of pancake batter. This filler (the colloidal silica) may be unnecessary, but I prefer to add it because it strengthens the epoxy bond but more importantly it makes it less runny, and thus doesn't drip through the holes I'm patching.
Once it's mixed, thoroughly, you now have about fifteen minutes to use it before it hardens in the bucket.

How to Patch Small- to Medium-Sized Holes
Small holes are great because you can just slather some thickened epoxy over them. But many of my holes were larger than a quarter, so I had to use the fiberglass.
It's a good idea to cut your fiberglass cloth into the appropriately sized pieces before you mix the epoxy. First, slather some epoxy around the hole to be patched, then apply the piece of fiberglass cloth, then slather more epoxy on top. You don't need much--just enough to fill the gaps between the threads, and to hold it in place. Once it cures, it'll be waterproof.
Repeat as necessary.
How to Patch Large Holes
This is why I saved the sheet metal from the walls and ceiling. Using a grinder, I cut patches of this metal to fit the holes left behind when I removed the bus lights. Then I applied a layer of silicone sealant around the edges (just be sure it's water proof), and applied the metal patch over the hole using bolts to secure it in place. This by itself would probably be fine, but not for me.
I then applied epoxy around the edges, and layered some fiberglass cloth on top, and then applied more epoxy, such that the edges of the patch were completely sealed and secure.

The inside, post-patching

Once It's Cured...
I think it's a good idea to give it a good sanding with a random orbital sander to smooth out the rough edges, particularly if you used fiberglass cloth. It's gonna look a little wonky, but that's why we paint our busses
after we finish patching everything.
Common Gotchas
- Mixing too much epoxy at once, and having it cure in the pot before getting around to using it
- It is essential to thoroughly clean the area in which epoxy will be applied--use acetone or some other solvent to wipe it down
- Applying too much epoxy, allowing it to drip where it shouldn't--you must clean it up immediately, before it cures, with acetone or (preferably) xylene. Once it cures, good luck removing it.