This is the method I use to etch double sided circuit boards at home. I've been using various methods for the past few months and have settled on this one, which I find to be the most reliable way to get both sides to line up.
What you'll need:
Iso-Propyl Alcohol (if you've got it)
Acetone (nail polish remover)
Rotary Tool (Dremel etc)
Plastic or Glass container
Most of this stuff you should have lying around or can borrow from friends/work. The Copper Clad Boards, Alcohol and Liquid Tin is easy to pick up from Maplins or Rapid.
Step 1: PCB Design
You can design your PCB in anything you want. A lot of people use EAGLE, but I prefer to do it in Adobe Illustrator. It doesn't matter what you use, these tips should still help.
If you're designing double sided boards you'll want to have a few holes somewhere that you can use to align both sides. I usually add an extra centimeter around the edge and put a small hole in each corner (this also gives room for a bit of error when etching).
You'll want to flip/mirror the front image so it is the right way around when you transfer it onto the copper. If you've done the back as if you were looking straight through then you don't have to flip that side.
The most important thing in my opinion is to fill in all blank areas black. When you're ironing it onto the copper the black areas will stick to the board, making it easier to iron and harder to rip/crease.
Once your design is complete, do a test print on normal paper and check everything is OK, then when you're ready feed a page of the magazine paper through the laser printer and print it out (I find thin, flimsy magazine paper is the best).
Step 2: Preparing the Board
I usually print out a test page onto normal paper to check everything is OK before using Magazine paper. I then use this to cut the raw board to shape.
Use masking tape to fix the paper in place, then cut it out using your rotary tool and the cutting disk attachment. It should make easy work of the fiber board, just make sure you try to keep the disk vertical and the lines as straight as you can.
Next you'll need to prep the board for transfer. You can do this many ways, but I prefer to give it a quick clean with washing up liquid, then use really fine grade sand paper to take the top layer off, rinse it under a cold tap, then using a scouring sponge and some alcohol I give it a last go over before rinsing it off again and drying with a clean towel.
The aim is to have a really smooth, blemish free surface with no grease (so watch those fingers!)
Step 3: Toner Transfer
Now you have to transfer the toner on the magazine paper to the copper board.
Make sure your copper board is as clean as possible and don't handle it too much and also make sure your iron is as hot as possible but with the steam function turned off.
I have started etching one side at a time because I think it's easier to line the two sides up. So start with putting the cut out from the magazine face down on the copper and holding one side (with a towel) start pressing the iron down hard. Once the paper starts sticking to the copper you can then iron outwards from that spot until it's all stuck tight.
I like to spend about 15 minutes on this, making sure it's totally stuck. Once you're happy that it's not moving around/creasing etc, press really hard and rub all over with the tip to really make sure its on there. This might take a bit of practice to get it right, so print plenty of pages out. If it doesn't work, get the acetone out, rub it off and start again.
Once you think it's done (you can usually see the design through the paper) stick it in a bowl of cold water and leave to soak for a minute or two. Then start rubbing the paper gently until it starts to come off. I prefer not to peel it off as I think the rubbing works a bit better.
If you're doing double sided boards, now is the time to drill the four alignment holes with a 0.8mm bit so you can align the other side afterwards.
Step 4: Etching
Before you start to etch, double check all the traces and make sure everything worked. If it didn't you can always use a Sharpie marker pen to fill in what was missed. Also if you're doing double sided boards, get some brown box tape and cover the back in it (make sure you cover the alignment holes on the front as well). This will stop the ferric chloride getting anywhere near the bit you don't want to etch yet.
Now it's time to etch; Get you Ferric Chloride balls and mix with hot water in your etching tray/glass dish. Place your board face up in the solution and rock the tray back and forth, always keeping the liquid moving over the top. This could take a while depending on your mixture, but you'll be able to tell when the copper has been eroded fully and you can see the fiberglass below.
When it's done, take it out and wash under cold water. You can leave the solution for the other side later.
Step 5: Remove Toner
This can be an awful job if you don't have any acetone, so I really suggest you going down to your local pharmacy (Boots will do in the UK) and get some Nail Polish Remover!
Just remove the Brown tape from the board and got at it with an abrassive pad and the acetone and you should get it off in a minute or two!
Thats one side done, if you want to do the other you'll need to clean the back the same as stage 2, then piercing the graphics with a pin or drill bit, guide it into place using the alignment holes. Iron this side exactly the same as stage 3, don't forget to cover the side thats already been etched in brown tape (as well as the alignment holes) then start stage 4's etching process again.
Once you have removed the tape and toner from the back, you'll be left with a beautiful double sided PCB. It's not quite finished yet though...
Step 6: Drilling & Tinning
You'll now need to drill all the holes in the board. I suggest getting a drill press accessory for your dremel to do this, although I'm sure you could do it fine with a steady hand and a bit of patience.
I drilled all the LED/cable holes with a 0.8mm bit and the screw holes with M3 bit. Then using the cutting disk I cut the board to shape and finished the curved bits off with a tubular sanding bit.
Moving onto the last stage we'll need to clean the board ready for tinning (making it look a pretty silver while stopping the copper from oxidizing over time). I use the fine sand paper again and finish off with an abrasive pad & alcohol.
Fill your tray with enough Liquid Tin to cover the board and gently rock it back and forth. You should see the copper start turning silver immediately, but give it a few minutes to finish off before washing the whole thing under the cold tap.
Step 7: Finished!
It might take you a bit of experimentation to get it right or come up with your own way of making PCBs, but it's really not difficult at all! I'd never even considered making my own boards before, but now it's made my controller project actually possible to finish!
Now all thats needed is for you to solder your parts on and connect it up to whatever project you're doing.