How to Record a Pay Adjustment from Customer

Im a partner in a small trucking company, we ran under this customer for a few months and each week before sending a payment, pay adjustments were taken out for fuel, insurance, and plates to run under this company. What hit the bank account was the net earnings after these pay adjustments. I was told that the pay adjustments should be counted as expenses for tax purposes. Question is, how do you account for these pay adjustments in quickbooks online without impacting you operating bank account? Is there some other account I need to set up to account for these pay adjustments/expenses?