You'd design the chip using a schematic capture program. The databook listed dozens of units that you could use, from gates to counters, adders, or registers. You'd send the design to Fujitsu, where software would layout the chip and they'd manufacture it.
http://www.bitsavers.org/components/fujitsu/_dataBooks/1989_Fujitsu_CMOS_Channeled_Gate_Arrays_Data_Book.pdf
Around the edges of the chip, bond wires connect the chip to the external pins. Special I/O cells allow the pins to be used as inputs or outputs. These cells are much larger than the regular cells to provide the high currents necessary to communicate with the outside world.