Personally i've never had any problems with updating a bios on a gigabyte motherboard using either the windows tool or through DOS.
If you buy a higher end motherboard (such as the Gigabyte GA-990FXA-UD3) it should receive bios updates to support future cpu's, can't guarantee that but that's what generally happens .
I have never used a UEFI bios before though, so i cant really comment on them, i suspect though the procedure isn't to different (i could be totally wrong about that though).
As for microATX motherboards, do they even exist with the 990fx chipset? i can't seem to find any.
The ones i can find seem to be low end low cost boards.