So I have a FAO debt because I made a silly mistake when I misread my forms in 2011. It's being paid off with a payment plan, but will they automatically take my tax return as well? Or can I ask them not to because I'm paying it fortnightly?

Yes, they will withhold your tax return to cover the FAO debt. The difference obviously will be returned to you, so if your debt is less than your return, they will give you back the difference.