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I recommend reading through
http://wiki.ros.org/urdf/XML/model,
http://wiki.ros.org/urdf/XML/joint,
and http://wiki.ros.org/urdf/XML/link
if you have not already.
joints represent connections between link / reference frames:
origin rpy attribute: "Represents the rotation around fixed axis: first roll around x, then pitch around y and finally yaw around z. All angles are specified in radians" (Tait-Bryan xyz extrinsic rotations) relative to the parent link's reference frame (effectively the parent joint).
origin xyz attribute: Represents the x, y, z translation relative to the parent link's reference frame (effectively the parent joint).
links represent rigid bodies:
origin rpy attribute: "Represents the rotation around fixed axis: first roll around x, then pitch around y and finally yaw around z. All angles are specified in radians" (Tait-Bryan xyz extrinsic rotations) relative to the parent joint.
origin xyz attribute: Represents the x, y, z translation relative to the parent joint.
If you want to be confused: https://en.wikipedia.org/wiki/Euler_angles#Tait-Bryan_angles
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