there are two possibilities. first the chip is probably "mask programmed" which means theres an etch mask use during the fabrication of the chip that makes the programming permanent, or second, . the chip is programmed through a JTAG interface, and the jtag pins connect to the test pads on the board. one thing you probably won't be able to identify is the chip itself because it's mounted directly on the PCB, the bond wires are bonded to the board and the chip, and then the thing is covered with a blob of epoxy. programming, if done by JTAG is done on a "bed of nails" fixture, where the board is pressed down on pogo pins, and held by some type of clamp. the pogo pins supply power, interface with the JTAG port, and there may be other pins for testing the functionality of the board at the same time.