Just as in a knife pleat, you stitch only the fell. The pleats are left open below the bottom of the fell.

The loops that you've flattened into box pleats on the wrong side of the kilt are held in place at the bottom of the fell by steeking, but, as Wally says, the steeking is done differently than in a knife pleated kilt (because there isn't enough thickness to stitch without going through tio the front side of the kilt). At the bottom of the fell on the inside of the kilt, just stitch the two adjacent folds together with a couple of stitches, carry the thread across the pleat, and stitch again at the bottom of the next fell. Continue carrying and stitching across the back. Repeat about halfway up the pleat.

Don't cut out the pleats. Just put on a stabilizer (yes - that holds the pleats at the top), and cover the whole thing with canvas and lining.