I've installed ceramic wall tiles in 22 bathrooms so far, but I have yet to set my first floor tile. However, it's not possible to understand the gameplan in wall tiling without also being able to understand the gameplan when it comes to setting floor tiles. Here's my advice. See if it makes sense to you. Confirm everything I say with someone who's knowledge and advice you trust, and by comparing view points, you'll learn enough to walk away with your own informed opinions.
The purpose in putting down a thin layer of something over your plywood subfloor is so that you don't start spreading a mortar bed directly on your plywood subfloor. That's cuz the subfloor goes UNDER your walls, and so if you make a mess of your subfloor, you can seriously damage your house.
Here's how they build a floor:
1. IN THE BEGINNING, there were the floor joists
2. Over the floor joists, they nailed, screwed, glued and screwed (take your pick) a lumber or plywood subfloor.
3. On top of that subfloor, they built the walls out of 2X4's
4. Then, they nailed or stapled down thin plywood underlayment inside each room.
5. Then they drywalled and painted,
6. And then they installed the flooring in each room, and nailed the baseboards on.
If you don't have any underlayment under your carpet, then that plywood you're looking at is your subfloor, and you don't want to do anything that might wreck it, like trowel a really flexible (meaning it has lots and lots and lots of glue in it) thin set mortar onto it. (It's the large amount of "additive" (pronounced "adhesive") content that makes these high performance thin sets flexible, but it also makes it stick like chewing gum to the underside of a church pew, and much harder to remove.) You don't want to put ANYTHING on your subfloor that will put of a real fight to remove.
By using a thin plywood over your subfloor, you don't have to worry about getting the thin set off. You can pry up the thin plywood and get back to a clean plywood subfloor relatively easily should you want to. (That's one of the benefits of having underlayment in each room of your house. You can always avoid having to remove the glue that might be holding an old worn out flooring down by replacing the underlayment.)
The way people recommend prepping the floor is to spread thin set on the floor and lay cement board (I recommend Hardibacker Board for a floor) into that wet thin set. The purpose in doing this is to fill in any dips in the floor where the cement board otherwise wouldn't be supported. That way, there are no soft spots in the floor where the grout would otherwise crack. You leave a small gap between the cement board panels, but this gap is not to allow for expansion since the cement board panels are very dimensionally stable.
The reason you need the cement board is that wood swells and shrinks with changes in it's moisture content, and ceramic tile thin set or grout simply doesn't have the elasticity to accomodate movement of the substrate. So, by putting cement board down, you're thin setting the tile to a dimensionally stable surface. There may be lots of stress between the plywood subfloor and the cement board panels, but there won't be any stress between the tiling and the cement board panels underneath, and that's what matters because that's what puts stress on the grout joints. It's exactly like standing on the fault line the day before the earth quake. There may be plenty of stress in the ground a mile below your feet, but you don't feel anything at all cuz the ground directly below your feet isn't moving. Since the cement board panels don't expand or contract, the grout joints of your tiling don't feel any tension or compression, and therefore don't have any excuse to crack.
Then, you fill the joints between the cement board units with thin set and put fiberglass mesh over the joints. Alternatively, you can put the fiberglass mesh over the joints first and then fill them with thin set. The purpose in doing this is to bond the neighboring cement board panels together so that (as it was explained to me by Custom Building Products (who make Wonderboard) "the whole cement board assembly is locked together and acts as a single surface", which I presume means that there can't be any relative movement between cement board panels.
Then, if you're using a porous tile, you seal the tops of your tiles with a sealer.
Then you trowel thin set on the cement board panels and set your tiles. (I suppose you could wait to set the tiles before sealing them, but you're likely to have sealer dripping down the edges of the tile, and I don't know if that would prevent the grout from sticking to the edges of the tiles.)
Then you grout your tiles, relying on the sealer to prevent any grout from getting into the porous surface of the tile and discolouring it.
You wipe the excess grout off with damp sponges until all that's left is grout haze. Then, after a few hours when the tiling is dry, you wipe the grout haze off with a DRY towel. (And, since the grout will be hardening up while you're working, don't mix more grout than you can comfortably apply in half an hour or so. AND, keep a green or white Scotchbrite pad handy so that if the grout does start hardening up faster than you can get it off with a damp sponge, you can tear it off in a hurry with a Scotchbrite pad without harming the tile surface.)
Then you wait as long as possible and then seal your grout, the dryer the grout, the better. The kind of grout sealer you want to use depends on where your grout is. On a bathroom wall, I'd use a penetrating sealer. On a kitchen floor (and for most floors I expect) I'd use an ACRYLIC film forming sealer like Glaze N' Seal's "Grout Sealer":
Stay away from any grout sealer that contains any kind of "siloxane" in the list of contents on the back of the bottle. That word means that it's a silicone based grout sealer, which should be taken off the market. Silicone based grout sealers work well, but the problem is that nothing sticks well to silicone based products (grout sealer or caulk) and so you can't apply another coat of grout sealer over what you have when it starts to wear off. (You can apply more silicone based grout sealer, but the 2nd coat won't stick well to the first coat.) You're much better off getting an ACRYLIC grout sealer so that you can apply additional coats as necessary to better maintain the protection on your grout for many years (or as long as necessary).
You want to use a film forming grout sealer to prevent liquids spilled on the floor from causing any stains or soft food from getting "mooshed" into the porous grout and providing a food source for bacteria. With an acrylic film forming grout sealer, then if push comes to shove, you can always strip the grout sealer off the grout with some acetone, and paint on more grout sealer. If you moosh peanut butter into porous grout underfoot, then about all you can do is have at 'er with a toothbrush and hope you get it all out. Either that, or try removing the affected grout and regrouting that spot.
Hope I answered some of your questions.