To track change orders separately in the budget, it is reasonable to create a new line item for the change order. This can be done by:
Select the budget where you wish to add the change order
Click on Add line-item > Add custom
Fill in the data
The change order was added to the budget
Now you can track the new change order to track its costs/income.
Note: depending on your project and budget structure, you might want to create a whole category for change orders to track them with more granularity for more detailed overview.