This is how I did our bathroom floor.

Prep: The bathroon had 2 different flooring materials. Tiles in the shower/toilet area and hardwood flooring in the sink area. The tiles in the bathroom floor were cracking and coming up, plus had some uneven spots. The previous tiles were put down directly on loose concrete. There was hardwood flooring in the sink section of the bathroom, which I wanted to salvage for repairs in other areas of the house.
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You can see the piece meal tiling
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See the cracks in the tiles and grout
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Had a friend come over and we pulled up the hardwood floor by cutting with the skill saw set to the right depth to just get thru the wood, but not damage the floor boards underneath. Those boards were used to fix some spots in the bedroom that need repairs. Since the wood is tongue and groove and nailed, using 2 people and a couple of pry bars worked well, to carefully as possible remove the wood. Of course some of the tongue and groove and pieces just didn't make it. Kim even helped a bi with the concrete removal. After pulling up the hardwoods we had to remove the 1980's concrete with the wire mess in it. The concrete was about 2 inches deep. Do not buy the long scrapper with a blade on the end, it was useless, instead use a small pry bar that can get under the tar paper, and a hammer to pry up the pieces. This creates a lot of dust.
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Once that was done I found that when they put the hardwoods in they put an extra layer of flooring in on top of the subfloor to even out the level with the thick concrete. Unfortunately they also put it under the vanity. I didn't want to take the vanity out so I bought more plywood to even out the level of the floor where the concrete was removed (shower area).
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I put thin set between the cracks where the boards met and in spots the floor wasn't level. It took about a day and 1/2 to dry.
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I used concrete board in the shower area and hardibacker in the sink area. Not because of special needs or anything. Just happened that mom had an extra sheet and some pieces that I could use. Kathy then picked up hardibacker. After working with both, I actually like the hardibacker better. It was less 'crumbly' and I was able to score both and bend/break perfectly. For the toilet flange, I measured out the edges, drew a box then found a circle that went slightly over the flange and used that for a template to draw the circle in the box, scored it with a box cutter knife, and punched it out. In this case it was the trash can in that bathroom. Again, putting thinset in the cracks and a couple of spots that weren't level. I used gray here, because I had gray and white. I knew this was going to be very thin, so used the gray to save the white for when I put the tiles down. I didn't want to risk any bleed through of the lighter color grout. Make sure it all dries well.
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Time to start working with the tile. Planning, planning, planning. I made a slight mistake, I should have started with the small toilet area as I ended out with a small piece that I had to cut unfortunately, but it's not too bad.
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The first row is the most important the rest will be success or fail based off the first row. Should try to get a full tile in the doorway, I had big tiles, and a small room, so did the best I could. Mixed the thin set a little thicker than pancake mix. Mix it well so you get as much of the powder smooth as possible. Put the thin set down, spread, use v shape portion of trowel at a 45 degree angle, to groove and keep consistent. Do the same on the back of each tile, put down the tile, use spacers to make sure position is right, and press down, move on to the next tile and/or row. If you have a spot that is not level, put some extra mortar in to help level it out. This is a little trickier since you can't groove it very well on the floor more than likely. I did have a spot like this in the shower area. To cut the tile use a wet saw, and take your time measuring and doing all cuts. It took me 3 tiles (wasted) to get it right around the toilet, I was tired and couldn't think. I did work from the doorway in. I wanted to make sure that everything was straight from the start with no gotcha on that end, would rather have an oops by the toilet. I made a little bridge to go from the hall as far as I could into the bathroom to avoid stepping on the tiles as much as possible. Now make sure it dries well, before doing the grout.
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To cut the tile use a wet saw, and take your time measuring and doing all cuts. I did work from the doorway in. I wanted to make sure that everything was straight from the start with no gotcha on that end, would rather have an oops by the toilet. I made a little bridge with a couple stools, and a 2x4, to go from the hall as far as I could into the bathroom to avoid stepping on the tiles as much as possible.
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It took me 3 tiles (wasted) to get it right around the toilet, I was tired and couldn't think. Now let it completely dry, and grout. Mix the grout according the directions and spread. Make sure you change the water frequently, I used big sponges. Afterward go back over and make sure you clean all the tiles thoroughly several times to remove the haze the grout leaves behind.
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Now put the baseboards in and choose if you want quarter round or not. I chose not to since everything was so white and the tiles were cut nicely to the wall.
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