Waist: Measure around your waist (over your shirt, not over your shorts) at the position where you normally wear your shorts. Keep the tape a bit loose, so it is comfortable.
Inner Leg: Measure along the inner leg seam of a pair of tailored shorts that you feel comfortable. The short hem should be about 6cm below the ankle bone. All Anthony Squires shorts have a 6cm turnup and 8cm back seam inlay, so alteration (if necessary) is quite straight forward.