How am I able to automate AVR ISP programming?
Command-line tools can be used to drive your programming tool from within a custom script.  A common one for AVR programming is "AVRDude" which allows full control of all aspects of programming AVRs including setting fuses and verifying the programmed firmware.  I have used AVRDude successfully with AVRISP MKII and BusPirate hardware programmers before.

I have only used AVRDude under linux but I believe it can be used in windows/mac as well.