Linings are a great way to check fit one last time. Breeches should be tight. Make sure that the crouch seam is snug against the nether regions. Whip or tack the linings with big (one inch) stitches. If everything looks good, transfer any changes to the body and cut the lining back open.
Turn the breeches inside out and back stitch the inner seams and press them open. Pull the linings together and line up their folded edges. Whip these closed. Make sure the outer and inner seams line up. If the leg seams start twisting use this to help resolve the problem.
What happens without a lining? Here are the bearer and the unfolded fall extension, back stitched to either side of a future fall cut. This is the front of a pair of linen Summer breeches. Seam allowance is only an eighth of an inch. More on how these go together is here at my old blog.