Laying floor tile requires a solid underlayment so the tiles don't move and crack. Normally, you should lay cement board over the existing floor before laying the tile. In some situations, that will raise the level of the floor more than you want to. There are circumstances under which you can lay tile directly on existing floorboards: when the existing boards are very solid and smooth, with no cracks or loose areas, and in rooms that will remain dry (not bathrooms). It's important to seal the floor with a sealing primer as a moisture barrier.
Walk the whole floor and look for any loose spots in the boards. Hammer in ring-shank floor nails anywhere you find any movement, making sure to hammer the nails completely flat.
Thoroughly clean the floor. Roll a layer of sealing primer over the whole surface, using your floor roller. Let it set for 48 hours.
Stretch a chalk snapline across the middle of the floor in one direction, hooking the end of it to the edge of the floorboard (or have a helper hold it). Pull back on the string about one inch and snap it, making a chalk line on the floor. Stretch it in the other direction, through the middle of the floor and perpendicular to the first one. Before you snap it, set your square at the intersection between the chalk line and the string. Adjust the string so it's at 90 degrees. Snap the line.
Spread thinset mortar over the intersection of the lines, using your notched trowel. Cover enough area to set four tiles in the four corners where the lines meet. Put spacers between the tiles as you set them.
Continue applying mortar and pressing tiles, working your way out toward the walls and using the lines as guides. Cut tiles to fit by the walls as necessary, using your tile cutter. Let the tiles set overnight.
Pull out the tile spacers. Apply grout over the tiles with your grout float, pressing it into the spaces between the tiles. Use the edge of the float to squeeze it off the tile surface. Wipe off the excess grout by running a damp sponge across the surface.
Wear protective eye goggles when using a tile cutter.