If you're scanning to GIF or PNG formats, you will need to scan at 96 dpi and for any other format, you scan at 72 dpi to keep your fabric in scale. This setting is in your scanner software - the interface pops up when you push the scan button on your scanner or when you acquire by TWAIN in an image editing program. (most people have Photoshop Elements or Paint Shop Pro, but you might have something else.
The default resolution is probably set to 200 or 300 dpi in your scanner, so you need to find where to override that in your scanner interface.
When the image is scanned and open in your image editor, check in "Image Information" or "Image Properties" to see that the image is 72 or 96 dpi, then do whatever tweaking you want to do to the image and then crop it to the size you want.
If the image is not the 72 or 96 dpi that you want it to be, change it to the correct resolution but check the option to "Maintain Original Print Size" or something similar. Then go on to the tweaking and cropping.
The EQ help files suggest cropping the scan to 3" square to keep the file sizes small, but I think I'd rather scan a whole repeat if I can. It does make your computer and EQ run slower to have large fabric images, though.
I've been saving 8" quilt blocks as fabric and dropping them into blank blocks on my Civil War quilt so that the quilt layout uses the exact blocks that I'm making. You really do notice the difference in performance.