We booked our bags most of the time between SJPdP and Burgos. The initial days I booked on the interwebs, because we were more certain of our distances. We mostly used Jacotrans and then phoned up the day before to book the bags, I think once you phone before 6pm. You put th emoney in an envelope attached to your backpack. Some hostels have envelopes from about 4 different transport companies. Never had a problem, although once they did phone me up as I had put the wrong hostel down on the booking form and they didn't have a booking for me, so I was able to tell the drive where I was really staying.
In terms of booking hostels, we have usually booked them, the initial one in advance, but the later ones a day or three before. I would have a rough plan for the stages we want to do and do some research about the different hostels, so I would know mostly where we wanted to stay, but only phone up 2 days before. Some particular ones I booked, like the Quatro Cantones in Belorado, which has a swimming pool, and Franziskaner beer (a heavenly afternoon). We walked early June.