You should direct this question to the person who will actually be making your kilt.
A simple phone call or check on the kiltmakers website should give you the answer you are looking for.
Each kiltmaker uses a slightly different method for measuring, so go with what they say even if it means sending two different measurements to each maker.

And be sure you tell the kiltmaker how and where you took the measurements.
You may want the waist on your kilt to be up at traditional height(covering the short ribs), at mid-rise, and even hip-hugger or low rise. Your kiltmaker needs to know this.


For example; Some kiltmakers measure for the waist at the top of the crest of the hipbone and them add 1" to find the natural waist and then 2 more inches for the rise. (This is for a Traditional fit kilt.)
Another kiltmaker may use the naval to find the natural waist.

For the hem, some have you kneel and then subtract to get the kilt to hit at the top of the knee, and some ask you to take the measurement where you actually want the hem to hit.

Then there are us Contemporary Kiltmakers who throw all the rules out the window and measure where ever you tell us to.

So the best advice is, TALK TO YOUR KILTMAKER! And use their system.