I'd say since it's your first time installing Cat6, increase your labor cost by 40-60%, and after you've done a few you could drop it down. If I actually had to do bids, I would probably be down to just adding 10% or less for labor.
Other than that, it really isn't all that different. I would second the suggestion of getting some hands on training from the vendor you decide to bid. Most vendors are changing the layout on patch panels and jacks. That way you will have seen the difference before you get to the job site.
Justin T. Clausen
Physical Layer Implementation
California State University, Monterey Bay