Basting the stitches before storing the kilt isn't a bad idea. It definitely would help keep all the pleats in place. I'd recommend folding the kilt with the pleats out, not in, as Rathdown describes, again, to keep the pleats neat. Folding with the pleats in tends to wrinkle the pleats more.

If you can store the kilt hanging, rather than lying flat, that would also keep the pleats neat.

And I will only say that cedar smells far better than mothballs. Every year at Burns Dinners I inevitably end up shaking hands with a number of gentlemen who reek of camphor, and I can't help but think "well, someone hasn't worn their kilt since Burns Night last year..." But whichever you use, it ought to be changed once per year.