According to the MSRPs on Cannondale's site, it's more than $300 more. Is your LBS discounting it heavily?

According to Cannondale's site, the MRAP is $1119 for the CAAD9 6 and $1799 for the Six Carbon 6. If you're getting the Six Carbon 6 for $1400 it seems like a decent deal.

The CAAD frames are still very highly regarded though and I suspect they're selling extremely well. Even though they're not carbon, they're US made and are race-grade frames. It's hard to say if it's worth it or not, which fits you better? Not sure what resale is on the Six, but CAAD frames have been selling at pretty high prices on eBay.