This is exactly, what I did. I moved bootloader and atmosphere folder to my harddrive and inserted the unzipped hekate and atmosphere folder to my sd. After that, I copied my bootloader/hekate_ipl.ini and bootloader/res to SD.
This is, how my bootloader looks like.
Code:bootloader ├── hekate_ipl.ini ├── ini ├── patches.ini ├── payloads │ ├── Lockpick_RCM.bin │ └── TegraExplorer.bin ├── res │ ├── eckig │ │ ├── icon_atmosphere.bmp │ │ ├── icon_atmosphere_hekate.bmp │ │ ├── icon_stock.bmp │ │ ├── icon_switch_logo.bmp │ │ └── icon_sysmmc_cfw.bmp │ ├── icon_payload.bmp │ ├── icon_switch.bmp │ └── rund │ ├── icon_atmosphere.bmp │ └── icon_switch.bmp ├── sys │ ├── emummc.kipm │ ├── l4t │ │ ├── bpmpfw_b01.bin │ │ ├── mtc_tbl_b01.bin │ │ ├── sc7entry.bin │ │ ├── sc7exit_b01.bin │ │ └── sc7exit.bin │ ├── libsys_lp0.bso │ ├── libsys_minerva.bso │ ├── nyx.bin │ ├── res.pak │ └── thk.bin └── update.bin
Since you got "Failed to init or mount SD" does hekate see your SD card?