I don't know that's there's any functional advantage to wearing a kilt at your natural waist. It would be the proper, traditional way to have it made, if that's important to you. If it's not, and if you already know you find it comfortable to wear your kilts at your jeans waist, then I think you should go with what you know. Definitely have this discussion with your kiltmaker and be sure that you're both on the page.

As far as buckles, I think a lower rise kilt looks much better with only one buckle on the right. The shorter fell looks a little crowded to my eye with two straps.