I currently owe the taxation department about $1000. I am currently repaying this through a payment arrangement. Will this money be deducted from my tax return, or will my payment plan continue as normal?
You have had to lodge a tax return to get the debt in the first place but that's the last of it - in terms of needing to input the amount anywhere.
Further repayments of debt (whether in part or in full) will not go towards any future Returns. BUT any interest you accumulate along the way - will be a deduction within your future Returns.