Hi Sam,
Go ahead and set it at the 6 ohm setting. All AV receivers are a bit different some have settings for 4, and some for 6. Impedance is a bit confusing with speakers because it varies accross the frequency response range. The minimum impedance is the frequency where the amplifier sees the lowest impedance or most resistance from the speaker. The nominal frequency is what is considered to be average impedance. It is best to match your receiver with the nominal impedance of your speakers.
In your case with your zone 2 speakers you can set them at 6 ohms even if they are 8 ohm speakers. Your amp will actually put out a bit more power when set at 6 ohms so it won't have a problem driving them.
The only time you really need to worry about impedance is when you are atempting to drive a 4 ohm speaker with an amp that is rated at 8 ohms. The amp will do it, but if you drive it really hard, the amp will either clip or go into protection and shut down as it overheats.
Cheers,
John Wanderscheid