Lodging is in or near downtown Boquete [1] unless otherwise specified. There are some good options in the outlying area, but those without their own transportation may find getting around inconvenient. Hostels and other backpacker-friendly places are more plentiful than they used to be, and there are quite a few pleasant, economical options for those on a modest budget.
Private homes are increasingly posting room-for-rent signs in front of their houses. These tend to be pretty basic. A number of the more upscale places periodically offer great rates for those who book through their websites; be sure to check. Hotel rooms can get booked up in Boquete, particularly during major festivals [2]. Make reservations well in advance if possible.
Links:
[1] http://www.moon.com/destinations/panama/western-highlands/boquete
[2] http://www.moon.com/destinations/panama/western-highlands/boquete/entertainment-and-events