How can I get my (Arduino) Pro Micro schematic to allow me to program it through GPIO instead of USB I'm trying this project so far I've got the schematic of a Pro Micro, which is powered through GPIO from a Raspberry Pi Zero, and want to remove the micro usb connection and able to flash it using an avr programer and a few pins. 

How do I get to Achieve that? also the Pro Micro is getting D+/D- from the the raspberry's D+/D- pads as well. Schematic below for reference.
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.