Bravo Calibration

Hi Everyone

I have made some progress with my Bravo unit which is pleasing although there are certainly parts of it i don't like.  For example it seems the only way for the throttle, mixture, pitch axis is to use the P3D menu and subsequently being able to easily move from aircraft to aircraft if going from a turboprop to a jet is time consuming but the biggest issue i have is a calibration issue.  

I have the PMDG B737 and profile activated and can use the throttles effectively however the Flap lever is a problem.  Fully up on the hardware is always giving me only flaps 1 not up no matter what I do and full down gives flaps 30 not flaps 40.  

Can anyone help with this calibration issue?  Do i try and calibrate in p3d or through the drivers.  Another thing is when the calibration software says leave the axis in a neutral setting, am i supposed to guess when the throttles, props and mixture are in the middle of their range or should it be at idle or full forward given its not a yoke?