I've now made several PCBs using the magazine toner transfer method. The same technique can be used to make double-sided PCBs (if you start with double-sided copper-clad board) but it is tricky to get the two sides lined up correctly, especially on larger boards. Here is a trick I found to make it easier.
When making the PCB design, make a row of squares of "copper" on the page off to one side, the same on both sides. When you print out the transfers these squares will become squares of toner. Put the two pages together, toner-side to toner-side and hold them up to a bright light. Adjust them until you can see that the squares are in the same place on both pages. Then, a quick press with the hot iron will melt the toner and stick the two aligned pages together. Then you can slip the board in between the two pages, iron on both sides and it should come out nicely aligned.