The current bootloader supports both reading from and writing to EEPROM through the STK500 protocol. Avrdude has an interactive mode that does a half-decent (DOS like) interface for reading/writing eeprom (screen or file) which is quite useful if needed.
The Arduino IDE will aslo produce an EEPROM image when you compile a sketch with EEPROM tagged data. Upload of this image however is manual.
So the tools are there if you learn to use them, but it most certainly would not hurt with an IDE integrated viewer/upload/download extension (e.g. graphical).
I have had a frustrating play with the Arduino GUI,
I found EEMEM mentioned in the forum as being supported in v13 and I am using v18 so I had high hopes, but no joy when I tried it.
The compiler sees EEMEM as an identifier, not a memory modifier like 'static'.
There is no mention on arduino.cc of EEMEM outside the forums and a playground request that it be fixed :(.
Found doc for PROGMEM and tried that (including avr/pgmspace.h as specified) and have the same issue.
Search the arduino-018 installation for EEMEM/ mentioned only in readme.txt.
Search for PROGEM, mentioned in HTML and bootloaders, tone.cpp, pins_arduio.[c,h] and Tone.cpp.
I guess something is broken:(
I suspect compiler issue/ but this version is ok [based on google search]
avr-gcc --version
avr-gcc (GCC) 4.3.2