How can I get the bootloader on the actual microcontroller to accept a 20Mhz crystal to I can upload sketches through my USB port as I used to?
The bootloader has no control over clock speed. Just swap out the 16MHz crystal for the 20MHz, and the ATmega will run at 20MHz. The bootloader has no way of telling what speed it is running at so you don't need to worry about what speeds it will "accept".
One thing you will have to watch out for is that the different clock speed will mess with delay, delayMicroseconds and millis.