Pay run didnt deduct the amount from my main account, I then reported pay as expenses and balanced acc but now i have two wage deductions on my p/l and its not accurate?

Hi lordofthethings-,

Thanks for posting in the Community! The posting of the amounts on your pay run will be based on the default accounts you've set for payroll. Let's check the default payment account you've assigned for payroll. 

1. Go to Employees tab and select Payroll Settings. 
2. Select Chart of Accounts.
3. Select Default Accounts to reveal the assigned accounts.
4. See Payment account selected. This account is often called the "Payroll Clearing" account and is used to reconcile the net payment amount of the payroll to the transaction from your bank account.

If the payment account is set to Payroll Clearing, you can match it to your bank feed by adding an expense transaction and allocate it to your Payroll Clearing account. This will create a transaction to debit the bank account and credit the Payroll Clearing account. 

After adding the payment(s), the Payroll Clearing account should have a balance of zero. To verify this,

1. Go to Settings ⚙ and select Chart of Accounts.
2. Find the account name and select Account history.

For more detailed information, you can check on this article: Matching payroll payments in QuickBooks Online. 

Feel free to drop a comment below if you need further assistance. I'll be around to help.