Hi there Kate Loubert,
It's important that all your transactions are entered correctly for your books to be well balanced. QuickBooks Online Payroll is a great tool able to help you pay your employees for their hours worked, all while entering this pay in your books. I can point you in the right direction for assistance with deductions.
For assistance with deductions calculating too little, or too much on pay runs, I recommend reaching out to the QuickBooks Online support team outside of the Community. They'll be able to best assist you in making sure that all your transactions have the correct deductions calculated, and provide steps to resolving the issue with the deductions overcalculating. You can reach them using these steps:
Schedule a Callback or start a Chat: click (?)Help in the upper right > type and enter "Contact support" into the QB Assistant > click Contact Us > explain your situation > click Let's Talk > choose Get a callback or Start a Chat.
Social Media: Facebook and X / Twitter
Ifyou have any other questions, feel free to reach out here.