You'll need to build an RS-232-C interface to convert from the TTL levels on J10/J11 to RS-232-C to hook it to a PC. There is info on doing this on the webpage below.
Then, you can attach GDB to the monitor built into the webpal and overwrite that with whatever you want....once you've done that of course, you can't go back!
It is safer to have two webpals if you want to do this. Then, you can always keep one flash with the original monitor code (and then you switch to the other flash while the system is powered up, just before you program it. That way you can also reprogram a second time if things go wrong.
I built a programmer since I like to build hardware as much as I like programming and I learned about how flash is programmed.
I've offered to program people's flash with the bootstrap + Linux. You'll still need to supply some sort of IDE device with a root partition. Email me at the address on my webpage below if you are interested.