CrossRoads:
"would it still allow me to program and send it over to the arduino through the IDE?""File:Upload Using Programmer" is part of the IDE.
It is just a different path for getting programs into the uC - instead of the Serial Rx/Tx pins, it uses the SPI pins.
You connect a AVR ISP to the board instead of using the onboard USB/Serial adapter.
After uploading the bootloader then can i switch back to the USB since my program sends commands/listens to the Arduino serial?