A trick I use on a program I wrote to run on an ATtiny4313 to enter a setup mode was to configure a pin that was normally use as an output as an input for a few seconds after power up. The pin was biased high or low via a resistor to select between normal mode and setup mode. (The resistor is required so that when the pin is in its normal state as an output pulling it high or low via the resistor has no effect.)
A few other points. Are the two versions of the board IDENTICAL other than the code in the ATmega8 ? If the ATmega8 is a plug in device why not just carry spares of both versions of the code. (An ATmega8 only costs about £2.00)
Les.