These registers are not used by the programmer. Data is moved around inside the chip by switching logic elements in a way consistent with carrying out an instruction. An example would be in connecting the various general purpose registers to the ALU.
Do not forget that a microprocessor is a hardware device. Software is merely a list of easily-modifiable instructions that control the signals applied to the hardware elements. A single software instruction is merely a pattern of bits that cause certain signals to be applied in an appropriate sequence.
Perhaps you should resort to Google for information on microprocessor architectures.