On my FXDC the shifter was adjusted so that it was about even with the toe of my boot, such that I rode with my foot splayed out, naturally, alongside the shifter, when I rode in traffic and anticipated shifting. In this way, I could stretch my foot down, a little, to get it under the shifter, for upshifts, or move my foot forward, getting some of my heel on the peg, raising my boot, a little to get it over the shifter, for downshifting. Otherwise I rode with my foot slightly aft of having the heel behind the peg, so as to avoid touching the shifter with the toe of my boot.
Some boots have tall toe boxes; this exacerbates the problem such that, if you adjust the shifter so you can easily get the toe under the shifter, for upshifts, you must then lift your entire leg to get the toe over the shifter, for downshifts. If the boot's ankle area resists ankle flex, then you're stuck lifting your leg which, incidentally, can lead to cramping, especially on long trips in heavy traffic, where you're continually shifting.