Arduino Leonardo uses its own bootloader, whereas ATMEGA32U4-AU comes from the factory with the USB DFU bootloader. With the Arduino Leonardo bootloader, avrdude uploads firmware (but not a new bootloader) using USB directly. The ATMEGA32U4-AU pin numbers start at the corner with the dot, and go around the IC counterclockwise (1-11 from the dot counterclockwise, then 12-22, then 23-33, and finally 34-44), when looking at the chip soldered to the board.
To replace the bootloader, you can use either the JTAG interface (PF4/TCK, PF5/TMS, PF6/TDO, PF7/TDI) plus /RESET, or the ICSP interface (PB1/SCK, PB2/MOSI, PB3/MISO, /RESET). I'm assuming you are using the ICSP interface.
The 6-pin and 10-pin ICSP connector headers, when you look at the connector with pins towards your eyes (NOT the female connector with holes), are
┌── ──┐ ┌──── ────┐
│ R C I │ │ I C R . O │ R=RST C=SCK I=MISO
│ G O V │ │ G G G G V │ G=GND V=VCC O=MOSI
└───────┘ └───────────┘
Please check your board with a multimeter, when the board is not powered, that these are connected to the correct pins on the ATMEGA32U4-AU: R=13, C=9, I=11, O=10, G=15,23,35,43, V=14,34. It is easy to accidentally confuse the MISO/MOSI pins, and to trust pin header numbering – but in the above text diagrams, pin 1 is top right, 2 bottom right, 5/9 top left, and 6/10 bottom left; these rarely match the pin numbering in connector footprints.
(If it is unclear, I too am a hobbyist, having made a booboo hereabouts myself.)