Using Serial Monitor with Pocket AVR Programmer or bootloading with FTDI Basic B

Hi guys
Working on a small circuit containing a ATmega328 chip that will need to be bootloaded and I don't want to use an arduino to bootload it. From what I can tell the Pocket AVR Programmer is the best option to do this.
I need to be able to set values in EEPROM over the life of the device via inputs from a PC, previously I planned to do this via Serial monitor but I assume I can only use serial monitor if I use the FTDI basic breakout board.
There is only room for one of these devices yet I don't seem to be able to do both jobs with one board.
Is there any program out there that will work with the Pocket AVR Programmer to let me send data to it from some kind of console?

Arduino, Pocket AVR, what does it matter when you are just going to connect a Programmer via cable to do the bootloading/fuse setting and then remove the cable?

Loading EEPROM:
Perhaps Atmel AVR Studio, I've only used it with Atmel AVR ISP MKii tho.
Likely there are avrdude commands as well, I've never tried that.

What I've done:
Have connections to connect an external FTDI Basic, you can have your sketch look for an outside command, and when seen accept any data and put it in EEPROM. Then only connect up when needed.

Or give it an uSD socket and feed it data that way. They're pretty small and flat.

How about this: