Most often, the thrust angle is built into the model's firewall, especially with trainers.

The actual way to measure the thrust angle is to first establish the fuselage as being level, then attach a meter to the crankshaft. This will give you the downthrust angle. Then, the fuselage is affixed in a jig to hold it parallel to the gound, and the same meter will give the side thrust angle.

A simple meter can be made with a 3rd grader's protractor, a piece of brass tube, a string and a weight. Tube size is chozen to most closely fit over the engine's crankshaft. (get a cupe of sizes too large and you can use the next couple of smaller sizes to space it down... it'll fit bigger engines later) The tube is affixed to the protractor such that when the tube is parallel to the ground, the 90 deg mark is straight down. The string is threaded through the centering hole, and the weight tied on the end. The brass tube slides onto the crankshaft. If the tube as a sloppy fit ont he crankshaft... a couple of wraps with scotch tape will snug it up.

The actual angle listed in the instructions is never really perfect due to the inherant minor misalignments in a model... so don't work yorself to death to get it exact. If an adjustment is found to be needed later, the mount alignment can be shimmed with thin brass sheet. Flight testing is needed to determine if the thrustline needs adjustment. (and we rarely bother with adjusting it on trainers... as long as its reasonably close.)