Loading bootloader directly over USB

So I've created what is essentially my own Arduino, using the MEGA2560 schematics for some testing and to learn more about the process. I'm using an AtMEGA2560 and AtMEGA8U. My goal is to begin by loading the bootloader on to the AtMEGA8U2. However, I've recently discovered something quite unfortunate. I've made PCBs without ICSP pin headers.

But I do have a USB connection. Is it at all possible to load a bootloader directly onto the 8U2 over USB? Or do I need to have on some pin headers somehow and use an AVR programmer?

I think the 8u2 firmware can be loaded over USB. http://arduino.cc/en/Hacking/DFUProgramming8U2

The ATmega2560 bootloader is usually written through the ISP pins. You need to connect to MISO, MOSI, SCK, Ground, Vcc, and Reset. Those are the six pins of the ISP connector (for ease of access) but each is also an Arduino pin.

Perhaps I was mistaken, but isn't there a way to load a bootloader onto the 8U2, and then the 8U2 does all the programming for the 2560?

If you have the DFU bootloader already installed on the 8U2, then you can upload new applications to the 8U2 via USB using (for example) the FLIP software from Atmel. If the 8U2 chip is blank, then you'll need access to the ISP pins to install any firmware (such as the bootloader, or a bootloader-less application).

The situation for the 2560 is similar: at first you need ISP to install the bootloader. Then, once the bootloader is installed, new applications can be uploaded via the serial pins.

As an aside, it is possible to turn the 8U2 into an ISP programer. See this thread:
http://arduino.cc/forum/index.php/topic,101690.0.html

So if I'm hearing correctly...You can load the 8U2 firmware over USB, but only if it already has firmware on it? And the 8U2 can load the 2560 firmware, but only if the 2560 has previously loaded firmware via ICSP pins?

I'll have a PCB with a blank 8U2 and blank 2560. At least I'm assuming they are blank straight from the manufacturer? And I have no ICSP pins on my board for either, so I can either solder tiny wires to those pins to give that access, or I'm out of luck?

Yes - solder tiny wires to those pins [SCK, MISO, MOSI, & Reset, Power, Gnd] to give that access.

Are you sure the pins aren't available at headers somewhere?

CrossRoads:
Yes - solder tiny wires to those pins [SCK, MISO, MOSI, & Reset, Power, Gnd] to give that access.

Are you sure the pins aren't available at headers somewhere?

I don't believe so, as I designed the PCB and forgot to add them. And I foresee soldering a single wire to a 0.5mm pitch IC as being quite the problem.

After checking the PCB, it looks like I can jerry rig the following access:

MEGA2560: MISO, MOSI, SCK, +5V, GND, and carefully touch a wire to reset (but no wire/pin access to the reset channel)

8U2: No easy access to any of the pins.

Is this enough to somehow get software onto both of these?

Only if you connected both chips up in parallel. If you can't access the SPI pins on the 8U2, you're out of luck.