IDK really, perhaps you can use a book.
I mainly did it in the 8085 practicals during B.Tech and they had a handy learning kit with a HEX keyboard so we could Assemble it manually on paper, write the program directly to a given RAM address and then run it from there. For ARM, we just used Keil µVision.
Now I just download an x64 instruction manual or just look up the instructions on the web, on the occasional requirement of reading disassembly.

I don't recommend starting with x86_64 reference. While it can be used just fine, it has lots of instructions and and you instead want a very small subset of them.

Also, there will be a great difference between using an OS and not doing so, as going with one, then includes a lot of potential boilerplate.