I was there a while back on my own boat. Beautiful group of almost completely undeveloped islands. There are a small number of islands with basic accommodation that you could stay on after your boat trip. They will likely be very basic, possible with electricity from solar panels and generators so don't expect much if any air conditioning.

In terms of the boat trip, I wouldn't plan on too many days aboard, it isn't like the BVI or USVI where most people are on vacation and get up everyday and go sailing, It is more a place where cruisers hang out at anchor for weeks on end. Unless the boat you hook up with is actually running a charter business under the radar, they'll likely want to set the itinerary.

Here's a link to the first entry in my wife's blog covering our time in... San Blas