Again, pardon my basic questions: What does the MBED chip do (2) What is ISP UART? (3) Can i not use the Bootloader in certain situations and as normal uart in certain? I am thinking i will load the program from a sd card (which i also have to figure how to load the program from the card to be sent to the "eprom"

Essentially the MBED chip is a device programmed to act like both a USB storage device and a programmer/debugger. It really helps during rapid prototyping as it take cares of a lot of little step. It uses UART0 to program the microcontroller by using the built in bootloader. ISP stands for "in system programming".

Yes, the benefit of the UART0 is it is a normal port until you enter the ISP mode. This can be done by shorting the correct pin to ground or calling the routines from code.

In regards to updating from a SD card you will probably need to do one of two things. Have/Make a bootloader program that reads the SD card and writes to the flash using IAP (In application programming) calls or have another microcontroller (similar to MBED) read the SD card and use ISP to update the main microcontroller. They both have their benefits and downfalls.

At the moment I do not have the time to locate a bunch of the resources you are looking for. But if you search Google or MBED for "MBED ISP bootloader" and "MBED bootloader from SD card" you will probably find all the same information. I will try to post what I have to help people in the future and I would encourage you post what you find useful to help others.