Step 1: Get ready
Anyway, once you have your design and paper, you will need to print the design. The key here is to mirror the top layer so that it will come out correct once transferred to the copper board. It can also help to include alignment marks (the T shaped things in the pic) beyond the edge of your PCB to help you align the two layers. See below.
Step 2: Align layers
Now, take the two paper pieces with the top and bottom layers printed on them and go to a window or patio door. It needs to be daytime since you will be using the backlight from outside to see through the paper. Place the bottom layer on the glass, and then taking care not to stick the top piece down yet, align the two paper sheets using the alignment marks, your vias, features or other method. When aligned, stick the top to the bottom. Carefully lift another corner of the top piece and add another roll of tape to keep the layers aligned. The key is to make sure the tape will not interfere with the copper board being placed between the sheets. See pic.
Step 3: Iron it on
Once you are done ironing, cut the paper around the board if desired, and drop the paper and board into a container of water to soak the paper. Let this soak for about 10 minutes. With the cheap glossy laser paper from Kinko's the time is much shorter than the high quality inkjet photo paper. Once the paper is soaked, peel the paper off both sides. This should leave the toner and a thin layer of the paper along with the glossy stuff on the copper board. Using your thumbs or an old toothbrush, carefully rub off the extra paper pulp and junk on the board. See pic, below showing a board with half of the pulp rubbed off.
Once the paper pulp is rubbed off, carefully inspect the traces and features on the board for small imperfections and stuff that will cause problems later. Key areas to pay attention to are closely spaced traces and pads where it is easy for paper or glossy coating to bridge and keep the copper from etching. Also, you can achieve very fine pads for doing TSSOP, QFP, and other fine pitch packages using the toner method if you carefully scrape between pads using an Xacto knife or similar prior to etching. During ironing, the toner tends to smear slightly, so very fine pitch pads tend to mush together. Using the knife, you can scrape between the pads or traces to make sure the copper will etch between. If you are careful, there is no reason you can't get 800 micron or even 500 micron pitch pads.
Step 4: Etch and clean
When the board is done etching, you need to get the board out and rinse it with lots of water. Dump the used etchant in your toilet and flush it as recommended by the manufacturer on the bottle. As you can see from the pic, you should be able to hold the board up to a light and see through the board at this point to verify the alignment of the top and bottom layers.
Cleaning off the toner is a pain in the butt. The easiest way is to use an aggressive solvent such as brake cleaner or acetone (nail polish remover) and a rag to rub the toner off. Using your preferred method, scrub the toner off the copper and get out your multimeter to test if any of the traces are shorted together. I find that long parallel traces often have small shorts between them if you don't get all the paper off prior to etching. A toothbrush helps. If you find that some traces or pads are shorted, then using an Xacto knife or similar, scrape or cut the copper until the circuit is open. Once all the circuit is verified in this manner, you can start soldering down the parts. I find that putting the fine pitch components down first is key, so that you can verify each pad as you go. Since the toner smooshes the pads of QFPs and TSSOPs and the like together, it is easy to form a solder bridge between pins. Take your time and have your solder wick handy.