Jumper -

There are some things that need to be cleared up about your question.

There is a fuselage reference/datum line, which is usually a horizontal centerline around which the structure of the aircraft is designed and built. The stabilizer is generally parallel to this line.

There is an engine thrust line which is a line that runs thru the crankshaft of the engine where a line on the plans may be drawn to represent the Thrust Line.

You may have a "horizontal thrust line" when these two lines coincide, but in most cases, the engine thrust line is adjusted to inprove the flying handling qualities of the aircraft.
Right thrust is used mostly to compensate for engine torque for conventional rotation engines.
Up thrust or down thrust is mostly used to compensate for pitch changes that accompany power changes. Generally the thrust line is adjusted so that it goes thru or slightly above the "vertical location of the CG". High wing airplanes generally have a higher vertical CG thus requiring downthrust; whereas low wing airplanes require little or no upthrust.

Got the picture?

Now if you can restate your question in terms of fuselage reference line (for measuring wing incidence angle) or engine thrust line (for measuring side and down thrust), then perhaps I can can have a better understanding of what you're asking.