I think you could do those the exact same way as the tutorial I linked, if you just ignore the "face" detail in the tutorial and apply the process to the shape pocket you want....I think it would have been a little easier if you hadn't put the skirt together yet, because then you could've incorporated the pockets into the side seams and waistband, BUT I see no reason why you couldn't still add them as full patch pockets.
I'd trace the pockets out the size and shape you want, add 1/4" seam allowance all the way around, and then cut out the pocket and lining fabric. Then sew as the tutorial describes.
Sadly, for the blue skirt, I do not have enough fabric... I want to try it out with a new one and then I wanted to try out what you explained (incorporate into waistband and side seams) but I am still frightened that I do something stupid. You all see only the nice photos of the finished object, not the sweating, swearing and frightened me during the sewing process :-DDD
But thank you so much for taking the time to explain: sewing and thinking 3-dimensional is tough for me (perhaps that's the reason I like to knit, it is so much slower, and I do not have to plan/understand so much beforehand)