I do a lot of upcycling. I try to rip seams when possible, but if I know I’ll have enough fabric (if I’m turning my husband’s pants into my toddler’s pants, for instance), I’ll often just cut right next to the seams instead of ripping a faux-flat fell + serged edge. I try to match up pants pattern pieces with the corresponding part of the real pants, so fronts on fronts, backs on backs – that helps with getting the grain aligned. Where possible, though, I try to avoid the areas that get the most wear so that the fabric isn’t already worn out.
I tend to rip pockets etc off first, and avoid that fabric if the wear is too different, or if there are holes (DH always rips the corners of his pockets). Generally I can avoid piecing anything but the waistband – I could probably salvage the original waist if I really tried, but generally I don’t bother, and just piece a new one together from the pants themselves.
In particular for jeans, you might want to try to cut your left and right pieces from the same locations on the left and right pant leg (that is, both front pieces cut from just above the knees on the front of the original pants, both back pieces cut just below the pockets on the back) so that the fading and wear more or less match. I’ve never made the after school pants, but my guess is that you’ll get more color variation due to the side panel and small panel at the ankle, but with some planning, you can probably make that look intentional!
Incidentally, I think upcycling pants is a little more difficult than upcycling shirts, due to all of the seams and tendency for rips/fabric thinning on pants. But it’s totally doable, and I always feel such satisfaction when I get second life out of something. Plus, my kid’s a toddler and hard on his clothes, so I don’t mind if the grain isn’t quite right, or the color variation isn’t uniform.