The best method for carpeting decking in an aluminum boat is to wrap the decking before installing it. Glue and wrap the individual deck panels so the carpet laps 2" around the back of the panel like this:
Then rivet or screw the panels in place through the carpet leaving the fastener exposed, this will allow you to remove your deck panels with having to rip up your carpet later on in case you develop a leak or have other below deck problems like livewell leaks and such.
With a little preplanning and measuring the exposed fasteners with add a detailed look ton your installation:
By wrapping the deck panels you will eliminate and joint/seams in the carpet that can wear, show through, and come loose after a couple of years.
JBC is right about the fumes from the carpet adhesive, read the precautions on the can label. Also pay close attention to the working temperatures for the adhesive written on the can.
A good carpet roller is worth it's weight in gold when installing carpet in a boat, I like this one:
http://www.homedepot.com/p/Roberts-Extendable-Floor-Roller-10-955/100012074
It will roll out any wrinkles and bubbles in the carpet and embed the carpet backing firmly in the adhesive for a more professional and longer lasting installation.
