Backup the content of your SD card, because you have no choice but formatting it with Hekate during the installation process. Once you are done, you can restore your files.
You shouldn't install it in first place if you know you aren't gonna keep it. But if that comes to happen, simply take the SD card out of your console and plug it into your PC, format the Android partition and integrate the now free space into your FAT partition. Is that easy.