The most common way is to attach stick on loops on your deck then loop bungy, rope or camstraps for securing of gear. Kayak style or auto shop small cargo nets are also a great option once you've created an anchor. get raft plug loops if you have an inflatable.
Products like NSI, EZ Plugs and Surftech's tie-down kit work well. Depending on your deck type (epoxy or rubber mat) some use epoxy to attach the plugs down if the default stick material isn't securing.
if you have the ability to glass in Leash Plugs, that's the most secure way to anchor to. they're also flush with your board when not in use.
check out a video i did for canoe kayak last summer on the subject..
http://stokemagazine.blogspot.com/2011/08/learn-how-to-pack-your-sup-for-trip.html (from my blog)
Cartop Kayak Carriers
Kayak Carrier Kits
Dock & Launch Systems
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