I do it all on the epson software before I scan. I have used the presets to make scanned areas which roughly correspond to my chips. I use 1.68 x 1.68 for chips and 1.59 x 1.59 for tokens. I preview the entire scanner bed (usually with a bunch of chips). I move the preset square over the chip I want and use the zoom function where I can center the chip/token and see if it is aligned properly. Thanks to Terry S., I now try to keep my chip scans square. With the Epson, I also keep them uniform size (266 dpi and 48-bit color), which makes the scans on the board the same size. Since I have scanned over time on different scanners, some of my scan do not line up perfectly, but that's ok. The new ones do. You can see in the zoomed image if you are cutting off part of your chip. By the way, I never place chips, dice, playing cards or whatever all the way to the edges of the scanning surface. I have found that the images might get cut off. If you are scanning just a few chips, leave a good margin all of the way around them, and leave plenty of space between them.
I only use other software, such as Photoshop, when something goes wrong or gives me difficulty (I did use it when I used my Brother scanner).
And...have fun with it! It's a hobby. I hope this helps you.
Michael Siskin