I'd like to add a technique that I find makes this much, much easier.
Mount your camera on a tripod, if you have one, and point it straight down at the table. Put a piece of paper down on the table, and put the board on top of the paper. Trace the shape of the board onto the paper. Now make sure the board is lined up (this works well with square/rectangular boards, obviously) and take your first picture. Now flip the board, line up with the trace, and take picture #2.
If your board is a weird shape (assuming my brain is working properly right now) you could also trace with a heavy marker, and then flip the paper as well, and then line it up facing the other way. This might help when you go to mirror and line up the images. (Or am I doing this backwards? My spatial awareness is only good when something's right in front of me)
The reason this works better is both pictures are the same aspect ratio and size, which makes it much easier to line up once you flip the images around. Then follow the rest of the instructions to blend the images together and you're all done!