I think you read the measurments wrong. 5'6" is the same as a 5.5foot bed. (ie. 12 inches in a foot)
Good choice on the HD.
Here are BIGJ's and MMDs Reviews on the products
http://www.svtoffroad.com/showthread.php?8-Review-Bed-Rug-Bedcover-with-Tailgate-Step
http://www.svtoffroad.com/showthread.php?93-Review-Bakflip-Tonneau-Bed-Cover
For the bed-rug, the model numbers are as follows.
F-150 Super Crew (w/o factory step gate) 09-10 5.5'
BRQ04SCK
F-150 Super Crew (w/factory step gate) 09-10 5.5'
BRQ09SCSGK
For the Bakflip, it will be the 5.5foot / 5'6" / 66inch bed
04 - 10 F150 Super Crew S/B 66.00
35309 *
ALso, research these parts on Amazon. Type in "Bedrug BRQ04SCK" and it will bring it up. 9 times out of 10, it will be cheaper on there. Google some options as well. anything cheaper than whats on the bakflip site, let me know, i'm looking for one as well.
hope this helps