Ok, so once you have a final trouser length, you hem the trousers as you normally would, moving the lining out of the way. The lining then is clipped just barely as far as the seam allowance and brought back over the seam allowance as well as over the hem allowance.
It is slipped either on the edge of the lining, or you can slip stitch it as you would a jacket lining, leaving the lining a bit of give.
I like this technique because the hem looks better. If you serge the lining in right down into the hem allowance, you end up hemming the trousers through the lining, or just to the lining, which isn't as clean looking in my opinion.