AlaskaShooter nailed it.
I think the trip is worthwhile but essentially you have two options: Work with AMHS and get a locked in reserved schedule (and be at the dock in plenty of time for loading) or do the waitlist thing and be flexible. The waitlist approach is OK but doesn't allow too much freedom to do other activities in whichever town you're at.
It's entirely possible to get an itinerary wherein one rolls on at PR, does a change in Juneau, and rolls off in Valdez or Whitter just a relatively few days later...but that means stops of only a few hours (up to 12 max IIRC) at various places. I'd suggest outlining a rough idea of where you want to stop for how many days and working with AMHS to book that itinerary.
As noted above, cabins add $$ to the cost of the trip...but would be more than worth it IMNSHO during a summer trip.