I use the MP Navigator Ex. It scans the image and then you have an option to save it. You go to "Scan/Import", then click on Photos/Documents.
Then another window opens where you click "Open Scanner Driver". When you are in the scanner Driver window, you can set all of your options.
I normally hit "Preview" which scans the whole glass. Then you can take your cursor and double click and create a crop box just around the card that you want to scan. Then hit "Scan" and it will scan just that area. If I'm going to scan a lot of the same size cards, I'll tape a piece of paper around the area that I'm going to scan so that I know exactly where to place the cards and then I can continue to scan one after the other until I'm done.
there is an "Advanced Mode" tab in the upper right hand corner of the Scanner DRiver Window which allows you to specify dpi and corrections, etc. I don't have any corrections on mine.
Hope this helps. It seems complicated but I've got it to a point where I just put the card on the scanner and click Preview, set the box and then hit scan. Then save it where I want it.