This is a really good question and the answer isn't at all obvious. Generally all angles are relative to "center line" that runs through the fuselage from nose to tail. Generally, but not always that center line runs directly through the the center of the engine. On some aircraft this center line corresponds to some feature of the fuselage (for example the top longeron), but that's not always the case.

Anyway, you're first task is to prop the fuselage up so that the this center line is parallel to the floor/table/etc (and may sure to check that the floor/table/etc/ is also level). Once you've done that, you might even be able to eyeball whether or not you've got some upthrust. If you're lucking the firewall on your model will be exactly perpendicular to the center line. In which case, you can use a triangle to check whether the engine is tipped up, down, or is level.

There's also several specialized tools, for example, a laser angle finder. I have one but find it's rather difficult to use or read accurately.