There's no magic anywhere and 99.1% of it is documented.

IA-32e/AMD64 is basically an extension of IA-32/x86. What you're looking for is to understand the difference between real mode, 386 protected mode, PAE, paging and long mode because the registers, instructions, addressing and sizes of structures differ.

You can learn all of this by reading the Intel software manuals and digging into it yourself.

Tools you need (for non-Windows):

- gdb/lldb

- assemblers: yasm, nasm, binutils (contains "as")

Optional tools:

- IDA Pro

- Virtualization/emulation such as VMware Fusion/Workstation (because it supports being a gdbserver), VirtualBox or QEMU

- Intel's CPUID app

You also need good references like:

- the Intel manual set (a giant PDF or a collection of several) https://software.intel.com/en-us/articles/intel-sdm

- https://sandpile.org (fairly current)

- https://ref.x86asm.net (outdated by useful)

Another helpful exercise is writing a toy operating system in Rust or only assembly. https://osdev.org has many resources and guides.