There is no right way to do this. Whatever gets the results you're after, is the right way.
I typically pick a base Exposure which will be the bulk of the image, this goes on bottom.
The rest doesn't make a difference because you're going to mask anyways. Say I have a foreground, a building, and a sky. I need 3 exposures one of each. Well the building as my base goes on bottom. The others don't matter because the foreground will be masked and not interfere with the sky, like the sky will be masked and not interfere with the foreground. That's the whole point of masks.
What you might however want to look at is Luminance masks.
Basically go into your channels. Duplicate the RGB channel, then intersect it with itself, duplicate and repeat a few times. That will give you progressive light channels.
Then select the base and do invert selection Ctrl/Cmd+Shift+i and repeat the same steps. Now you'll have progressively darker channels.
Your base exposure still goes on the bottom but then you can save some time by using an appropriate luminance mask on however many additional exposure layers you have, then manually masking out / in parts that the luminance mask didn't get.