The commercial carpet squares you are talking about are not rated for outdoor or marine use. The glues that hold the carpet to the backing will break down under extended periods of moisture.
Go to your carpet store and ask for Beaulieu (Pronounced "Bull You") indoor/outdoor Vitality or Vigor styles with the Non Skid Marine rubber backing. These are 100% High UV Olefin, rated for marine use. They can be ordered in cut sizes 6' and 12' widths. They also come in a variety of colors including browns and tans.
Hope this helps.