How can I get my (Arduino) Pro Micro schematic to allow me to program it through GPIO instead of USB
Welcome to arduino.stackexchange.
You can program your ATmega32U4 on at least two ways:
1. Use Arduino's bootloader and D+/D- pins. This way you won't need an external programmer. Try search for phase "programming ATmega32U4 with bootloader".
2. Use ISP (In-System-Programming) method. In this case you can use your avr programmer. To do so you also need access to PINs named Reset, MISO, MOSI, SCLK. See this link or this one 

As always, the important read is ATMega32U4 datasheet.