Actually, it is not that difficult to mathematically determine a reasonable close approximation of the vertical CG of our models. And the more accurate you can estimate and/or measure the weight and determine the center of mass of the various components, the more accurate you can determine the vertical CG.
Establish some longitudinal reference line. Any will do, but the thrust line is usually already on the plans, so that will do. Then weigh each of the major components of the model. If the model has not been constructed, a fairly close estimate can normally be made of the painted wing, horizontal tail and fuselage. You should know the weight of the engine, muffler, wheels and LG legs/gear covers wheel pants or whatever other major components you have in the design. You should also be able to determine the approximate location of the CG of those components on their vertical axis. Measure the distance of that vertical CG position of each component relative to your reference line (the thrust line in our example) and multiply that distance by the component weight. You will then have a moment measured in inch-ounces for each component. (for English units, the terms can be in inch-ounces.) For those items that have their CG above the reference line, give those a positive moment. For those items below the CG, give them a negative moment. Add these moments and divide that value by the total weight of the components. You will get a linear measurement that represents fairly closely where you vertical CG will be relative to your reference line. It will be as accurate as your estimate of component weights that you cannot weigh and your estimate of the center of mass of those components. For the fuselage, you can come up with some guess as to its completed weight (painted) and an "eyeball" location of its vertical cg relative to the thrust line. With the engine/muffler, weigh the whole thing with the spinner and prop, then sort of do a balancing act with your fingers to see where its vertical CG is relative to the thrust line.
This approach works and can give you a very usefull initial point for your design vertical CG. You can then adjust various components, like primarily the wing, so that the leadouts will be very close to that vertical CG location. With the wing, you can simply move it up or down relative to the reference (thrust) line, or you can use combinations of different amounts of dihedral and vertical position of the chord line to get those leadouts where you need to have them. When you start adding dihedral, you need to compensate where the average chord is (or to be more precise where the mean chord is) relative to the reference longitudinal line. In other words, for a wing with dihedral, the wing center of mass will be above the root chord line.
Or, you can look at proven designs - with and without dihedral and those with different locations of of the wing relative to the thrust line to get you in the ball park of correct vertical CG postions, at least close enough to allow appropriate trim adjustments.
When you consider these calculations, it becomes easier to see why light or heavy wheels can make a big difference on the vertical cg location on the model. For example of a "typical" size and configured model (flat or no dihedral wing), let's say that your complete wing weighs 12 ounces, you can estimage that its center of mass is on the chord line and that chord line is, for example, 1 inch from the thrust line. (Other than the engine/muffler, LG components, horizontal tail and fuselage, the wing is one of the most significant weight components to determine the vertical CG.) So, we have a -12 inch-ounce moment. Now, let's say that the two wheels weigh 2 ounces total (these are heavy ones! The LG legs should be calculated separately) and the axles are 6 inches from the thrust line. So we have another -12 inch-ounce moment, the same as that huge wing that is 6 times the weight of the wheels. The combined moment of just those two components then becomes -24 inch-ounces, divide that by the total weight of those items (14 ounces) and you get their combined CG position (for just those two items) to be 1.7 inches from the thrust line.
In my opinion, it is easier to run these excursions on paper than it would be to make "cutouts" of the various components and, given the accuracy of your estimating capability, a more accurate determination of vertical CG than what "cutouts" will allow.
Something to ponder