Can anyone help me a 3D body rotation problem - I am trying to align the axes of a 9axis mIMU to a body segment so the angle output corresponds with interpretable information (e.g. joint flexion, abduction etc)

Apologies if there is a simple solution to this. I do not have a mathematical background and do appreciate rotations is not a straightforward topic. I have generated IMU orientation using the Madgwick filter - I can obtain the output in quaternions, euler angles and rotation matrices if necessary. I would simply like to manipulate the axis of the inertial coordinate system so it corresponds with an arbitrary body frame (e.g. humerus in anatomical position). I get the feeling converting both the 'state' (orientation output from filter) and the 'process' (rotation I would like to apply) to rotation matrices will be the best way. I have managed to do this, but not entirely sure how I apply the rotation to the position? Any help will be much appreciated!