I've found that scanning both sides and using photo software is good, but there's a better one.
I use the Corel Draw package, which includes Corel Photopaint to do the sizing/stretching to square, and so on. But then importing that into Corel Draw lets you put the top on one layer, the bottom on another layer, and use yet a third and fourth layers for drawing in first the pads, then the copper traces. CD lets you make layers invisible at a click, so you can turn off the top side and get the pads and traces right on the bottom, then turn off the bottom and traces, and fill in the top side.
It's even better if you think like a PCB layout guy.
In your draw program (or on your matte-surface mylar overlays if you're old-school) assign one layer to component bodies, one to pads, one to top side traces, and one to bottom side traces. Use two more for top and bottom scans. Work ENTIRELY from views that are from the top/component side of the board so you don't confuse yourself.
Make all the layers invisible except the bottom scan. The bottom should be mirrored so it views as though you're looking through the PCB. Stack the pads layer on top of the bottom-view layer, and put in color-filled circles for every pad. In through-hole boards, the pads will be on the top side as well.
When that's done, put the bottom traces layer on top of the pads layer and the bottom scan, and put in wide colored lines for the traces.
When that's done, click the bottom scan and bottom traces layer to invisible. Make the top layer visible below the pads layer. Now trace in all the traces you can see. Add to it all the traces that you can see by referring to the PCB with a magnifier or loupe. Then get out your ohmmeter and use needle-probes to trace out the remaining traces where they go under parts.
This is usually easy enough to do with through-hole stuff. If there is a via under the part, you'll already know it from the pads layer tracing. If you're careful, you can get all of it, or close enough to guess the rest.
Now all you need is a component layer. Turn off the pads and traces, leave the top side scan on and draw in component outlines.
When you get done, what you have left is the PCB layout. It can probably be manipulated to work as is for toner transfer, depending on how fussy you were with getting the photos the correct size and squashed-ness. Drawing the schematic is then pretty trivial.
But it's simple to use the layers you've traced as a guide and go into a layout program and place parts, then run traces on grid. The result is very suitable for etching.
It helps to understand the PCB layout frame of mind in tracing. I'm not tossing this in here for spam purposes because I sell a trunkload of them anyway, but if you want a quick guide to the PCB frame of mind, get a copy of my PCB Layout for Musical Effects book from Small Bear. It will not only teach you to do pro-quality layouts, but also improve your tracing by getting your mind right.