The true thrust line on any model is the difference between the stab incidence and the engine thrust. The measurement standard is what you want to find.

On my designs that standard is always the canopy base , I make it so it`s easy to find the reference because I`m constantly tweaking and learning new things.

Finding That standard can be done a few ways . If you have adjustable stabs ,you can use the motor set it to no more .5 down then measure the stabs if they are not at zero, set them to zero while the engine is at the standard of .5 neg. If the stab is not adjustable you may have better luck setting the standard with the stab at Zero and adjusting the engine thrust to .5 down. Then from there start with .5 positive in the wings.

If nothing is adjustable, Learn how to use a Dremel tool

If you have .5 neg in the engine and the airplane pulls to the canopy you have one of two problems, incidence in the wings are not enough, or the stabs are not perfectly aligned with each other may be the c/g is too far forward as well! It could also be a design problem or not enough incidence in the wings.
All this is explained in my trimming guide Here http://www.ckaero.net/blog/triangulation-trimming-2/

This is the forward to my Philosophy on trimming the 4 page laminated flow chart is where the rubber meets the road
and an easy to read field reference

Bryan