Make A Good Design First

A good plan will save you a lot of efforts and is the base for a good PCB. It is good to avoid too thin wires or wires too close to each other - you can not get the factory quality with this method.
Decide how the elements will be soldered to the board. If they will be on the same side with the printed wires, you need a mirrored image on the paper. This kind of element installation is easier, for you do not need to drill holes, and can make adjustments afterwards. Also, this way you get shortest connections.
The other way - with the elements on the opposite side, makes the device more mechanically durable.
The factory standard is double-sided PCB, but these are harder to make at home. The main hurdle is the precise alignment of the top and bottom layers – even a 1 mm gap is not acceptable.
If you are already good at making single-sided PCB, you can jump to the design of double-sided here.
If you want to stick with a single layer, there are some useful tricks.

You can have wires on the top layer, without actually etching them. Make them straight and as short as possible as jumpers.

PCB wires top layer

You can use the top layer as a ground plate.

PCB top layer ground plate

Note that this way, you have to prevent the elements, that are not connected to ground, to touch this plate. Use a bigger drill or Dremel tool to remove the copper around them.

There are different software options for creating PCB. I will show you a combination of Cadsoft Eagle and Gimp
The free version of Eagle has these main features: creates schematic and layout, run Autorouter, supports 2 Schematic Sheets, 2 Signal Layers and 100x80mm routing area. I suggest to use actual designs not bigger than this area and the reason is not only the free version limitation.
When you heat paper and PCB plate, they stretch to a different extent. The bigger the plate, the bigger the difference. This makes the toner to smear. I use Eagle to create the design and Gimp to make the file that can be printed on any computer and printer.
First, in Eagle, select the layers you want to be visible. Export the file as image 600 dpi, monochrome. The output file should be in .png format.
In Gimp, create a new file, corresponding to A4 standard, which is 210 x 297 millimetres/8.267 x 11.692 inches, with the same resolution as the exported image – 600 dpi. This makes a file 4961 pixels by 7016 pixels. Open the exported .png file with Gimp and copy/paste it on the A4 file as many times as it fits.

PCB Gimp printing A4 4961 pixels by 7016 pixels

This way, you can print more designs on one sheet of paper. You will see how useful it is, when the toner transfer would not be successful from the first attempt.
Next, go to File/Print/Image Settings and be sure to check “Ignore page margins”, otherwise the image will not match the actual dimensions of the design and elements.

PCB Gimp Printer Image Settings

Then go to File/Print/General and according to what you want, choose your printing device, or print to PDF file, in order to print it in a printer shop.

You are ready to hit print now. I advise you to use a special heat transfer paper to print your design.
You can experiment with other types – it is good to be glossy and not too thick, in order to transfer the toner easy.
The printer settings are also important: use resolution of 600 dpi or higher and find the right setting for the paper you are using. My HP printer gives best results with “Lable” setting.

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