@mikep91 For the SD card structure, see https://docs.duet3d.com/en/User_manual/RepRapFirmware/SD_card
You need to run the version of DWC that ships with the firmware. It would be better if you downloaded the zip file of the whole RRF 3.4.6 firmware release In the case of RRF 3.4.6, ie " Duet2and3Firmware-3.4.6.zip" from https://github.com/Duet3D/RepRapFirmware/releases/tag/3.4.6 which has all the files you need.
This includes the correct firmware for your Duet board, the correct version of DWC, the updated WiFi firmware, and the IAP binary file (In-application programmer), which is used to update the firmware when using DWC. See https://docs.duet3d.com/en/User_manual/RepRapFirmware/Updating_firmware#required-files
For a list of things you need to change from 2.x to 3.x, see https://docs.duet3d.com/User_manual/RepRapFirmware/Migration_RRF2_to_RRF3
Ian