Under the scanner page, you will want to make sure your scanner driver is selected, and choose a format for the scanned files you save. I like PNG for scanned files, but TIFF works just as well, or you can choose JPEG if you are willing to sacrifice some loss in quality for much smaller file sizes. If you choose JPEG, you will need to select a quality setting. 10 is a good compromise between quality and file size, but if you plan to do a lot of editing on your scanned images, you might want to go with the highest quality setting of 12, or choose PNG or TIFF which will be larger but won't lose quality. My preference is for PNG files because they usually come out about half the file size of TIFFs with no loss of quality.
And by now you're probably familiar with the "Save Files In" section... just click Browse to pick the folder where you want your scanned files to be saved. If your scanner allows multiple image scanning, all the images you scan will be named automatically and placed in this folder. Once you have them in the Organizer, you can always rename them or move them to another folder through the File menu.