In respect to EagleCAD, I use it all the time. Once you get used to it, it is pretty good. You can pull parts from a library, and you can download many other parts libraries as well. You can create a decent schematic, then make the PCB easily from the schematic. Once the PCB is drawn, simply print the image onto a piece of clear acetate or similar on a laser printer. Since laser printers are more expensive, many people don't have one. Simply print the PCB layout on normal paper, on an ink type printer, then take them to a print shop to transfer them to an acetate. This way, you can use the acetate as a mask to etch the PCB. When making a two sided board, I lay both acetates together, make sure it is aligned as you need it, then drill two small holes in opposite corners. Then, place the top acetate on a blank PCB, drill the two holes through the PCB, using the acetate as the template. When you stick two pins through the holes and the top acetate, you will automaticaly have the proper alignment to place the lower acetate. You can use through holes for components for the pins as well.
Sorry to speak beyond the actual PCB design software, but you indicated a hobby use. Many people like to gather hobby tricks, so I hope this helps you. I am assuming that you are planning to use photo etch boards? If not, then simply place a piece of carbon paper under the acetate, and do a stylus transfer, using the same pin technique. Either way, the main focus is to get both upper and lower sides of the board in as close alignment as possible. The pins will do this.