Firstly, in order to combat the smaller surface area of your feet you should spread them more widely than you would with a regular waterski. With a normal waterski the length of the ski means that if it points slightly outwards it then forces your leg down that path and ends with you doing the splits meaning the legs can’t be too far apart. With barefoot waterskiing however there is no such problem and you can space your feet out at a wider angle to spread your weight. Have them at about shoulder’s width apart and facing just outwards, and make sure that it’s your heels that touch the water which should cut through it without bending or hurting your feet. Make sure you also keep your knees slightly bent however, as if you have them straight you won’t have any control and they’ll be more likely to split or apart or slip out from under you.
At the same time you should keep a tight grip on the rope. Pull harder than you might when wakeboarding or waterskiing as this will take more of the weight and pressure off of the water and allow you to move your legs more freely.