eagle1703:
Where is your GPS mounted on the frame?  Are you using the little pole?  Can you post an image?
Here's  an example:  My GPS is mounted on the frame/arm screws on the right arm  of the hexa frame on about half the little pole height, call it 8cm  tall. I fly the F550 as an "X".
The calculated horizontal CG is the center of the top frame plate, using the battery to balance everything out.
So imagine a left/right line from the arms through the center of the top plate.  Any mount location forward of that line is a positive X value.  Behind, negative.
Imagine  a line through the center of the plate, front to rear.  Any location to  the right of that line, where I am, is positive. Left, negative.
The  vertical, "Z", measurement is a bit more guess work because you'll need  the "vertical CG" and it's probably the hardest to figure.  But say  right now, all you have on board is a battery, secured on the top frame  plate. If you held the hexa up by the front 2 arms, so the nose points  upward, it would probably want to tilt a little like it wants to fall  over on its back because of the motors and battery positions.  This  means your vertical CG is toward the top plate, instead of centered  between them.  Let's call that CG position about 1cm under the top frame  plate.
So add the height of the GPS puck above the top frame  plate to the 1cm and what do you get? Using the little pole, probably  something like 8-10cm.  Since any Z value above the CG is negative, the  number you enter for the Z axis in Assistant is "minus" 8-10cm.
My numbers are:
X=0 because I'm on the lateral line
Y= +8 because I'm 8cm right of the centerline
Z= -8 because I'm above the CG on a shortened pole
Ron