I have heard that there is some problems between this CPU and motherboard and that you may need to update the bios or flash the bios or something. I don't understand what either of these mean or how you do it. Will they both work out of the box or will i need to make some adjustments? Any help would be greatly appreciated.
You cant go wrong with the ASUS M5A97 R2.0 its excellent choice, due to the fact it affordable and better than the rest with its unique asus feature called : USB BIOS Flashback
this feature will allow you to update the BIOS without a CPU, just update BIOS using the motherboard and USB drive and power supply unit, so 100% this CPU will work with this motherboard if not, you can update the BIOS to the latest version that supports the pilediver series using the USB BIOS Flashback feature.
Plus the 6 phase VRM is more than enof for default clocks (iam the kinda person that does not like overclocking or dynamic overclocking like Turbo boost), cause this board have original support for AMD Phenom II quad cores and hexa cores and those CPU consume ~180 Watts and up., while the fx 6300 is around 60W idle ~160W Load
You will see that the first original version was: 0208
M5A97 R2.0 BIOS 0208
First release Bios
Now as weird as this sound i had an MSI motherboard (a75a-g35a) with outdated BIOS 1.0 and inserted APU a8-3850 and the system booted ??? although on there website they state that you need 1.3 BIOS version so i dont know whats up with that, i updated the BIOS ofcourse, however the system did boot fine using the outdated bios version ???
again what you need to do is either :
1) give it try without any BIOS updating cause the motherboard maybe shipped updated with the latest BIOS.
2) IF it didn't work research how to perform : USB BIOS Flashback