I've put together a comprehensive scanning video here. However, here are a few more points of caution when it comes to scanning.
1. TEST SCANNING IN ADVANCE! I have several folks in a panic each year who administer their semester exam, head down to scan, only to find that the scanner isn't working. They are then faced with a looming deadline to get grades entered. Please, please, please, test the scanner in advance to provide yourself some wiggle room.
2. The page below is important... really important. I'll admit that I typically breeze past this page when I'm printing bubble sheets. However, the pieces I've highlighted are very important. Paper size - typically it's 8 1/2 x11, however, if the assessment is long, it may need to be 8 1/2 x 16. Additionally, forgetting to click the "fit to page" button will almost certainly guarentee an impossible trip to the scanner.
3. Do yourself a favor and calibrate. I say it in the video, but wanted to reiterate again, calibration solves 95% of scanning issues. I recommend doing this before each scanning session.