The AutoISP mode is usable on the RS232 port only.
When particular hardware conditions are met (on RESET and PSEN* pins), the target device starts executing the bootloader program on reset.
AutoISP is the mechanism by which FLIP controls the boot process hardware conditions so that you do not have to manually set them.
To take advantage of this feature, you must design your hardware so that the RS232 / RTS signal is connected to the PSEN* pin and the RS232 / DTR signal is connected to the RESET one.
The AutoIsp mode may be activated through the Preferences dialog.