For studies that aim to assess biological ankle function, calculating ankle joint complex (AJC) power between the calcaneus and shank is recommended over conventional inverse dynamics estimates between a rigid-body foot and shank. However, when designing a new experiment, it remains unclear whether holes should be cut in footwear to permit motion tracking via skin-mounted markers, or whether marker placement locations should be tightly controlled across conditions. Here we provide data to assist researchers in answering these questions. We performed a gait analysis study of walking (0.8, 1.2, 1.6 m·s−1) and running (2.6, 2.8, 3.0 m·s−1) while subjects (N = 10) wore custom-modified footwear, which allowed markers to be placed either on the shoe, or on the skin via cut-out windows in the shoes. First, we compared foot markers affixed to the skin vs. on the same locations on the shoe. Using statistical non-parametric mapping techniques, we discovered that skin vs. shoe markers had no statistically significant effect on net AJC power estimates throughout stance phase, for all walking and running speeds. Second, we compared calcaneal markers in the nominal shoe configuration vs. markers in a nearby location (∼27 mm below) on the shoe. We observed significant differences when marker placement on the shoe was varied, which may be relevant to repeated-measures study designs. The results suggest that when computing AJC power for walking and running, you may want to put down the scissors (i.e., forego cutting holes in your footwear), and instead pick up a Sharpie® (pen) or use a template, to maintain consistent marker placement across trials and conditions.