Does this bypass all of the ROG SupremeFX software?
Not all some echo audio affects work if select headphone as device only but important things like equalizer etc work with both.
Do I need to use any specific settings on it with these speakers?
If you have 4.1 you can do tests to verify all speakers getting correct signals individually.
You can try all settings thats what they are for , some use bass boost others listen linear without any alterations it all indvidual and depend on sound system
I assume I use the headphone plug on the front of the Control Center from now on?
For headphones good to always use the front plug as it has opamp and better quality output than rear output.
For amplifier front also produces better sound.
Anything else that I should consider?
You can also set up so that headphones and rear work at same time then dont need to hear pop sound every time connecting headphones.
Will the forum bugs get fixed?