There may have been some negotiations with your client about the rates while creating the quote for a job. Those rates that were manually modified in the quote will only be reflected in the Active Quote, once it gets approved. But if your invoice will be based on the Actuals (i.e. what really happened) instead of the Quote/Budget, then those rates need to be copied into the Project’s Rate Card.
To enable this option, go to the fourth icon at the top left of the Budget window and under Add Budget Rates To Project Rate Card, select either Ask or Always.
Add Budget Rates To Project Rate Card
When this setting is changed from the Budget Window, there is a dialog reminding the User that the change only applies to that specific Project. New Projects will still have it set to the default option, according to the initial configuration in the Server Setup > Financial tab > Add Budget Rates To Project Rate Card (Default).
Only if the option was set to "Ask", when clicking OK in the Budget window, a new dialog asks: "Add Budget Rates To Rate Card?".
Select items for Rate Card
See here the resulting Rate Card.
You can enter a name for this Rate Card and click OK. Once you start scheduling these prices will apply over the default from the price list.
If you create this Rate Card after having added some bookings to the Project, then click on "Force Apply" button first. A dialog will ask "Do You Want To Reset All Object Prices To Their Original Prices?". Select 'No' to not touch those items which you had manually modified. Select 'Yes' for the system to refresh the prices on all items with the default price from the price list - this means that discounts or manual prices to any items in this Project will be removed.
The Rate Card dialog only opens if Budget is set to 'Active'.