I used the same carpet and glue as Waterwings did. It will adhere just fine to the aluminum, but if you ever want to remove it, you will find that you will have a LOT of work to get the aluminum looking acceptable again.
I did mine in about 30 sections, due to the fact that I had 7 hatches, all carpeted, and the lids, as well as more corners in my boat, in no real pattern, due to the decking shape. Total pain in the neck to do, unless you are doing large sections, and only have hatch lids in the middle (I put a hatch wherever I could, leaving me with 1 inch wide strips here, and 3 inches there, tapering up to 6 etc. Real pain to have a one inch strip on the end of a 4 x 6 foot section, without allowing a seam). I found that you can put a seam just fine on an inside corner, but you can't an outside corner. For your hatches, wrap all the way around to the bottom, not just the sides/top. If you can, leave it big, glue it in, let it sit for 45 minutes, stretch it and roll it with a rolling pin, then 2 days later, take a razor knife to the edge you need trimmed. Ends up a little better that way.