My grandfather (and by extension my dad) swore by the kneeling method. I think that this method generally results in too long a kilt. Also, we all have different knees, so I don't think it will always result in an accurate measurement. The best way is to have someone measure you from where you want the top to be to where you want the bottom edge to be. You will get lots of discussion on where people want the top to start and the bottom to end!
My own opinion (and it is just that, an opinion that applies to traditional kilts only) is that if you measure from your navel to the floor while kneeling, you will have a kilt that sits too low around your body and hangs too low on your knees.