As a very simple example, take
LDA #0
or for better visibility
LDA #$ED
In the first cycle, the LDA byte is read, comes in over the databus, and is steered to the IR. The PC is incremented.
In the second cycle, the control logic digests this byte, and sets things up. Also, the second byte comes in over the databus - this always happens, with no influence from what the opcode was. This operand is headed for the IDB, the internal databus.
In the third cycle, which overlaps with the fetch of the next instruction, the operand byte is now on the IDB, and is routed over the special bus SB through the decimal adjust logic to the accumulator A.
Have a good long look at this tabulation, in combination with Donald's block diagram:
http://visual6502.org/JSSim/expert.html ... loglevel=8The thing to understand is that the datapath is controlled by the datapath control signals, and they are derived from the outputs of the PLA. It's in the datapath that all the arithmetic, logic, and data movement happen.
It might help to draw out the sequence on several copies of the block diagram. With coloured pencils. Don't underestimate the power of pen and ink - it's enormously easier to think with pen and paper than with keyboard and screen. At least, it is for me.