Yes, you can just update directly to the latest firmware. I recommend using Daybreak. But you don't install or even re-install Atmosphere nor Hekate; they are just files you place on the SD card. You can download the latest version of Atmosphere from its
GitHub page and Hekate from its
respective site. If you pirate any games, you will also need to update your patches which you can do so by downloading the latest ones from this
thread. Lastly, delete any themes you may have installed as those are firmware-specific and will not function when you update your firmware.