I've read the instructions here:
and I'm very grateful that I have the option to directly program the MCU with my AVR-ISP. However, as I also program my regular arduino boards quite frequently, it would be nice to have a menu option to switch between these different options rather than have to drill down and edit the preferences.txt file each time. I would suggest adding a "Program Via" option in the Tools menu that would contain these options:
Bootloader (default) AVR ISP AVRISP mkII USBtinyISP Parallel Programmer
Just a thought.