Is that the Art of Kiltmaking I see in the corner of one photo? Or where are you getting your instructions? Most folks use the X-Kilt instructions for making their first kilt, especially with such a casual fabric. But I'm like you, jumped in to a knife pleat first thing, although with a fashion tartan in wool -- so it's not carved in stone that you make an X-Kilt first.

Are you machine sewing or hand stitching? If you have a machine, topstitching each pleat edge, inner and outer folds, will make your cotton behave better.

Not sure what you mean by "messy" along the waistline. The top edges will not be even throughout all the folds -- AoK mentions trimming them evenly before attaching waistband, IIRC.

It looks as if you have already hemmed it. You will want to go back and re-hem in a few areas, otherwise the different layers will not line up. You can see where the deep pleat is sticking out below the top apron, for example -- that hem will need to be taken up, then tapered to meet the rest of hemline. There's a thread here titled "bits of hem in a properly made kilt" or words to that effect, where Barb T shows what I'm talking about.

The fabric looks great and I hope it turns out well for you. Keep posting questions and the rabble here will provide all the help and support we can!