I just dive in and do things before I know that they shouldn't be done - I have put joins in but have always made it so the sewing line forms the inner fold of the pleat. I sew the join straight, so the pleat depth is greater at the top than the bottom due to the supression for the waist.

I found the seam distorted the pleat if I tried to put it anywhere else than the back fold.

I have had to cut off the selvages on a kilt made with pieces taken 'across the cloth' as they were 1/4 inch shorter than the rest of the fabric once it had hung for a while.

I make the pleats and check that the join is going to be correct before sewing it. I mean the pleats on each side should lie right without the join being sewn - if they don't before they certainly won't after.