Note: if you just want to adjust the bounding box size and initial camera height, please see this simpler FAQ entry instead.
In the Prepare->New scan menu, you can specify a config file. This is aimed at advanced users who want to configure Skanect is a more precise way. It follows the .ini file format, and it can be used to specify an arbitrary bounding box size, orientation, and initial position. The best way to document it is through a sample
;; Size of the bounding box, in meters
size-x = 2.5
size-y = 2.5
size-z = 4.5
;; The offset can adjust the initial position of the bounding box
;; The reference point is the bottom-left-back corner of the box.
;; The camera is always at 0,0,0 looking towards -Z (usual OpenGL convention)
offset-x = -1.25 ; half of size-x, horizontally centered
offset-y = -1.25 ; half of size-y, vertically centered
offset-z = -5.0 ; initial camera will be 50 cm in front of the box
;; An initial rotation of the bounding box can also be specified, in degrees.
;; The rotation is around the bounding box center.
rx = 0
ry = 0
rz = 0
Here we are defining a large bounding box for a corridor-like room, centering the initial position horizontally and vertically, and starting outside of the room. Below is a graphics showing the coordinate system conventions and explaining the various parameters.