Ive recently created a payrun that was not ment to be, but ive lodged this with the ATO. I know ican fix this in payruns, how will this affect whats already been lodged

Thanks for sharing the complete details of your concern, stevebruce141.

Since you have submitted the pay run and lodged it to ATO, you'll have to contact them.

They'll be able to check if you can still cancel the lodgement, so you can submit the pay run once more. However, if it went through successfully, you can request a correction.

Please contact our Customer Care Support Team, so we can assist you with entering the correction in QuickBooks Online.

1. Go to Help at the top and click the Contact us button.
2. Enter Support in the What can we help you with? box.
3. Hit the Let's talk button.
4. Select the icon for Chat or Get a callback.

To learn more about e-lodge with the ATO, please check this article: 

Enable BAS E-lodgement for QuickBooks.

I want to be your direct point of contact so we can get this taken care of so please let me know if you have any questions.