How do you eat an elephant? One mouthful at a time.
On the other hand, what is/are your goal CPU(s)?
If you're looking at the Intel/AMD family of CPUs, I'd start with the one that began the family, the 8080. That's small and simple enough, and you have a complete ecosystem of 8080 development with editors, compilers, linkers, etc. on CP/M emulators. Also the 8080 (and its bigger brother, the Z80) is small enough and simple enough to get all of the instruction-types (register operations, jumps both absolute and conditional, bit rotation, AND, OR, NOT, XOR logical operations, status flags, interrupts, etc, etc) under your belt.
There is a whole universe of 8080/Z80 software sources out there on the Web for you to analyse and reconfigure and rewrite.
The later Intel chips become more and more complex but basically used the same sort of operations in different ways. You get into stuff like memory management, multi-cores, multi-user, instruction-read-ahead, etc. that would confuse greatly somebody starting out. Best leave that gear for later.
But if you are looking at working on RISC CPUs instead, you could look at RISC-V which has several emulators for you to play with while learning the basics. It's also at a stage where you could possibly 'get in on the ground floor'.
RISC is a different mindset, less varied instructions in your usable set, so you just use more of them in different ways. Very offbeat analogy: Your car can't turn left, so you make it turn right 3 times.