Might be helpful, to take a step back, and for a short time, obtain an older book, or comprehensive manual.
The way I learned microprocessors was buying a specific book, considered near-obsolete, but still with full explanations of the internal BUS, and block diagrams how the various registers connect.
What is instruction 'FETCH', (?), questions like that, you should ideally have an intro.
I used the older book:
'The Z-80'. by Rodney Zaks, but also various other books covering the 6502, an older, much loved IC.
You could stare at the electrical stats, on the pin outs, all day, and still not comprehend the basics. In your device, maybe you wish to 'transfer' the contained data, over to some other register. You'd need to know, which instruction, in the uP set, that you should use.
Often it might look like what's called a 'move',
'MOV. R7, R10'
Things like that, where the instruction will copy the data from R7, and put the copy into R10.
You might have to just learn or get intro on an instruction set, by reading small portions at a time (you could ask here, if question).
Spec. will typically list how many clock cycles it takes, to do. Also, notice that the example I just gave doesn't affect any outputs, it's all internal for the one little transfer.