Alex,
I just used the regular indoor/outdoor carpet glue that I bought at Home Depot. Worked out OK so far. It's cheap and it allows you to work with the carpet for a little while before it sets.
I'm probably into it for about $1500. Sometimes I wonder when I see ads for a boat/trailer/motor for about the same price if I should have gone that route, but I had a lot of fun figuring this project out and put in the work. Here's by breakdown on major parts:
Boat...$350 (old Lopez Marina rental, he as more)
Trailer...$300 (Harbor Freight kit trailer, new)
Motor...$300 (1982 Johnson 15HP, runs good. Looking for a newer motor soon)
Supplies like lumber, carpet, etc...$200-$300. (Doesn't include tools that I buy high quality for future projects).
Then there are all the extras that seem to be "must haves" that add up fast. These are the ones my wife complains most about! Foot operated trolling motor (my old hand clamp on worked just fine!). Fish finder (need another one up front!) New tackle storage for what I can bring that got left behind in the kickboat! Come to think of it...I need some new rods/reels since I have all this extra room. ;)