That's kind of a funny story:
When I bought my first Tandem Island back in spring 2010, the first week out I got pulled over by the police, they had a Scarab and I tried to outrun them but couldn't (humor), (as Sarasota is the go fast boat capital, there are lots of really fast superboats, so the cops need to keep up I assume).
They didn't give me a ticket or anything, but said since The TI is over 16 ft long, it probably should be registered in Florida. I was planning to add an emergency gas motor anyway so I went down to the tag office to try and get a title and registration.
To make a long story short (too late) it was a 2-3 month ordeal, as nobody had apparently had ever tried to register their kayak before, and neither the tag office or the dealer knew what to do.
Finally we got it all worked out and got the Certification of origin from the dealer, and got everything worked out.
Now it's probably much easier, basically you ask the dealer when you buy the boat for the certificate, they give it to you, and you take it to the tag office along with the sales receipt (to make sure the state got their tax revenue). If you bought the boat from a private owner, make sure to get a receipt, and hopefully they have a copy of their original sales receipt, otherwise you might be liable for sales tax.
If you bought a used boat, without a certificate, you will need to go to a Hobie dealer with the HID (hull identification number, on the right rear of the hull), and they can hopefully help you get a ID certificate from Hobie, (without that certificate your pretty screwed, I'm a pretty good talker, and couldn't convince the state that they didn't need it, and just to give me a title and registration anyway).
Hopefully this helps you to ask the right questions, and get the proper documentation when getting your boat, as going in I sure didn't know any better.