Maybe I am old school, but I would go back with the original logo. It is a great design and it fits with the clean and classic look you have accomplished with the boat. Especially with something that is "permanent" like embroidery in upholstery.
Alternatively, I think it would be cool if you used a contrasting color for this part of the seat. Cover the seatback underneath with a solid color and then get your logo embroidered on a bound piece of upholstery with piping about the width of the logo and use some snaps or velcro to make the piece interchangable. That way you could have two of these, one with the factory logo design and one with your design. I hope that makes sense.
Kind of like the "waterfall" on a Corvette http://www.web-cars.com/images/vette_img/X05CH_CR080_a.jpg
With the piece that has the Corvette emblem being the snap in/snap out uphostery I am talking about in a contrasting color.
Another cool idea for graphics on the outside of the boat would be using that Century logo and doing a play off of the Nautique griffin graphics, but again your boat looks nice and clean as is.