In AZ Mode:
Save a Terrestrial User Object with Axis1=0, Axis2=0 (this represents North/Level)
Slew (Goto) this saved position, with tight clutches. Your encoders are now at (0, 0) North/Level
Loosen both clutches and move your MOUNT so that your OPTICS are pointing North/Level. Re-tighten your clutches. Now your mount and encoders are in sync.
Be mindful of your dovetail orientation, specifically if using an L-Bracket, or any other right-angle type of mounting to your optics, as this might change the direction your optics are pointing relative to the direction the mount is pointing. (your optics may be parallel, or perpendicular to the mounts dovetail) (scopes are often parallel, DSLR's are often perpendicular).
In EQ Mode:
Save a Terrestrial User Object with Axis1= -90, Axis2= 90 (this represents EQ Home)
Slew (Goto) this saved position, with tight clutches.
Loosen both clutches and move your MOUNT so that your OPTICS are pointing at the NCP (near Polaris). Re-tighten your clutches.