What Legion said. The info on the net is a bit confusing. I just dealt with that. But they're very helpful on the phone and you'll get the info you need.
The only high speed ferry I know is the Valdez to Whittier route, so normally you do the north to south route in 5 days or so. There are two ships running now from Bellingham. One has a 6 day layover in Juneau, the other only a 6 hour layover, and that wasn't clear from the website. To go to/from Whittier to Bellingham you have to change ships in Juneau. Call them for the summer schedule and whether there is a quicker ferry.
2007 R1200GS; 2006 DL650 V-Strom; 2011 F800R (sold); 2013 CRF250L (sold); 1995 R1100GS (sold); 2006 Ducati Multistrada 620 dark (sold); 2013 F800GS (woot!)