Hi good news there then. Wow, that was lucky, I must've guessed right for once!!
You should be able to use three sicks of memory in a dual channel configuration with modules inserted in DDR3_1, DDR3_3 and DDR3_2 as long as they are all a matching kit. Don't forget though if they came from an X58 board that the voltage is only 1.5v on hte new board so don't be tempted to use any XMP that they may have attached.
Personally I wouldn't use the Quick Boost utility as it is never as good as doing it properly through the BIOS and quite often these programs cause problems with something else.
They are working on the BIOS all the time at the moment so I can't see it being a problem for long.
You can flash your BIOS if you feel that you will gain something from it. You have a Backup BIOS so if anything does go wrong we can always reflash the Main BIOS with that one.